Last updated: 2022-03-30

Checks: 7 0

Knit directory: chipseq-cross-species/

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    Untracked:  output/qc/H3K4me3_E12.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_E13.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E13.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_E14.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E14.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_E15.5_overlap.frip
    Untracked:  output/qc/H3K4me3_E15.5_overlap_downSampled.frip
    Untracked:  output/qc/H3K4me3_overlap_default_dunnart_downSampled.frip
    Untracked:  output/qc/H3K4me3_overlap_p0.01_dunnart_downSampled.frip
    Untracked:  output/qc/slurmjob.stderr
    Untracked:  output/qc/slurmjob.stdout
    Untracked:  output/qc/ucsc_alignment/
    Untracked:  output/rnaseq/

Unstaged changes:
    Modified:   analysis/mouse_dunnart_peak_features.Rmd
    Modified:   code/basic_wrapper.slurm
    Modified:   output/qc/A-1_input.PPq30.flagstat.qc
    Modified:   output/qc/A-1_input.dedup.flagstat.qc
    Modified:   output/qc/A-1_input.dupmark.flagstat.qc
    Modified:   output/qc/A-1_input.unfiltered.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.PPq30.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.dedup.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.dupmark.flagstat.qc
    Modified:   output/qc/A-3_H3K27ac.unfiltered.flagstat.qc
    Modified:   output/qc/B-1_input.PPq30.flagstat.qc
    Modified:   output/qc/B-1_input.dedup.flagstat.qc
    Modified:   output/qc/B-1_input.dupmark.flagstat.qc
    Modified:   output/qc/B-1_input.unfiltered.flagstat.qc
    Modified:   output/qc/H3K4me3_overlap_default.frip

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/peak_level_comparisons.Rmd) and HTML (docs/peak_level_comparisons.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
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html	b3950cd	lecook	2022-03-30	Build site.
Rmd	6203f8e	lecook	2022-03-30	wflow_publish(“analysis/peak_level_comparisons.Rmd”)
Rmd	f5adfab	lecook	2022-03-30	wflow_publish(“analysis/peak_level_comparisons.Rmd”)
Rmd	a605c33	lecook	2022-03-16	updated
Rmd	757db1e	lecook	2022-03-15	updated
Rmd	a97d3c5	lecook	2022-03-01	first commit

Summary tables

After the tables is all the code to compare peaks between species using liftOver and bedtools. It is a lot of repetitive code that I could revise but it was easiest to track it all this way for now. The summary tables show the number of peaks for the different overlaps.

LiftOver of peak coordinates between species

All peaks with no peak width filtering

## Load modules
conda activate chip
module load ucsc

## Extract peak coordinates
less output/peaks/dunnart_enhancer_peaks.narrowPeak | awk '{print $1,$2,$3}' > output/peaks/dunnart_enhancer_peaks_coord.bed
less output/filtered_peaks/cluster1_dunnart_promoter_peaks.narrowPeak | awk '{print $1,$2,$3}' > output/filtered_peaks/dunnart_promoter_peaks_coord.bed

## LiftOver peak coordinates from dunnart to mouse
liftOver output/peaks/dunnart_enhancer_peaks_coord.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_smiCraTOmm10.bed output/liftover/dunnart_enhancer_smiCraTOmm10_unmapped.bed
liftOver output/filtered_peaks/dunnart_promoter_peaks_coord.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_smiCraTOmm10.bed output/liftover/dunnart_promoter_smiCraTOmm10_unmapped.bed

files <- list.files(liftover_dir, pattern = "dunnart_enhancer_smiCraTOmm10.bed|dunnart_promoter_smiCraTOmm10.bed", full.names = T)
files <- as.list(files)
data <- lapply(files, function(x) data.table::fread(x, header = FALSE, sep = "\t", quote = "", na.strings = c("", "NA")))

df <- data.table(enhancer_peaks_smiCraTOmm10 = dim(data[[1]])[1], promoter_peak_smiCraTOmm10 = dim(data[[2]])[1])

kable(df, caption="Table. Number of peaks lifted over from dunnart to mouse")

Table. Number of peaks lifted over from dunnart to mouse
enhancer_peaks_smiCraTOmm10	promoter_peak_smiCraTOmm10
916	55

LiftOver peak summits

Prepare peak summits and extract peak IDs


## Extract peak IDs
less output/peaks/dunnart_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}' | sort > output/peaks/dunnart_enhancer_peaks_IDs.txt
less output/filtered_peaks/cluster1_dunnart_promoter_peaks.narrowPeak | awk -F '\t' '{print $4}' | sort > output/filtered_peaks/dunnart_promoter_peaks_IDs.txt

less output/peaks/E10.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E10.5_enhancer_peaks_IDs.txt
less  output/peaks/E11.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E11.5_enhancer_peaks_IDs.txt
less  output/peaks/E12.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E12.5_enhancer_peaks_IDs.txt
less  output/peaks/E13.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E13.5_enhancer_peaks_IDs.txt
less  output/peaks/E14.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E14.5_enhancer_peaks_IDs.txt
less  output/peaks/E15.5_enhancer_peaks.narrowPeak | awk -F '\t' '{print $4}'  >  output/peaks/E15.5_enhancer_peaks_IDs.txt

less  output/filtered_peaks/E10_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}' > output/filtered_peaks/E10.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E11_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E11.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E12_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E12.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E13_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E13.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E14_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E14.5_promoter_peaks_IDs.txt
less  output/filtered_peaks/E15_cluster1_peaks.narrowPeak | awk -F '\t' '{print $4}'  > output/filtered_peaks/E15.5_promoter_peaks_IDs.txt

## Concatenate pooled summit peak files 

cat output/peaks/H3K4me3_pooled_macs2_default_summits.bed output/peaks/H3K27ac_pooled_macs2_default_summits.bed > output/peaks/H3K4me3_H3K27ac_dunnart_pooled_default_combinedSummits.bed

cat output/peaks/E10.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E10.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E10.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E11.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E11.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E11.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E12.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E12.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E12.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E13.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E13.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E13.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E14.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E14.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E14.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed
cat output/peaks/E15.5_H3K27ac.pooled.macs2_summits.bed output/peaks/E15.5_H3K4me3.pooled.macs2_summits.bed > output/peaks/E15.5_H3K27ac_H3K4me3.pooled.macs2_combinedSummits.bed

Extract rows from summits file based on enhancer and promoter peak IDs

files =list.files(fullPeak_dir, pattern= "macs2_combinedSummits.bed|default_combinedSummits.bed", full.names=T) # create list of files in directory
files = as.list(files)
summits = lapply(files, function(x) fread(x, header=FALSE, sep="\t", quote = "", na.strings=c("", "NA")))
names(summits) <- c("E10", "E11", "E12", "E13", "E14", "E15", "dunnart")

files2 =list.files(fullPeak_dir, pattern= "peaks_IDs.txt", full.names=T) # create list of files in directory
files3 = list.files(filterPeaks_dir, pattern = "peaks_IDs.txt", full.names=T)
files = append(files2, files3)
filenames <- sub('\\_peaks_IDs.txt$', '', basename(files)) 

files = as.list(files)

peak_IDs = lapply(files, function(x) fread(x, header=FALSE, sep="\t", quote = "", na.strings=c("", "NA")))
names(peak_IDs) <- filenames

filtered <- lapply(summits, function(x) x[x$V4 %in% unlist(as.vector(peak_IDs)),])
filtered <- lapply(filtered, function(x) substr(x$V4, 1, 13))

filtered_bind <- rbindlist(filtered,)
filtered_bind$V4 <- substr(filtered_bind$V4, 1,13)
filtered_split <- split(filtered_bind, by = "V4")

names(filtered_split) <- c("E10.5_enhancer", "E10.5_promoter", 
                           "E11.5_enhancer", "E11.5_promoter",
                           "E12.5_enhancer", "E12.5_promoter",
                           "E13.5_enhancer", "E13.5_promoter",
                           "E14.5_enhancer", "E14.5_promoter",
                           "E15.5_enhancer", "E15.5_promoter",
                           "dunnart_promoter", "dunnart_enhancer")

lapply(names(filtered_split), function(x) write.table(filtered_split[[x]], file=paste0("output/liftover/",x,"_summits", ".bed"), sep="\t", quote=FALSE, col.names=FALSE, row.names=FALSE))

Extend the summits 25bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 25 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_50bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 25 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_50bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_50bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_50bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_50bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 25 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_50bpsummits.bed

Extend the summits 50bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 50 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_100bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 50 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_100bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_100bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_100bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_100bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 50 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_100bpsummits.bed

Extend the summits 100bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 100 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_200bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 100 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_200bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_200bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_200bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_200bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 100 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_200bpsummits.bed

Extend the summits 150bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 150 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_300bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 150 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_300bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_300bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_300bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_300bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 150 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_300bpsummits.bed

Extend the summits 200bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 200 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_400bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 200 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_400bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_400bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_400bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_400bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 200 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_400bpsummits.bed

Extend the summits 250bp in both directions

bedtools slop -i output/liftover/dunnart_promoter_summits.bed -b 250 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_promoter_500bpsummits.bed

bedtools slop -i output/liftover/dunnart_enhancer_summits.bed -b 250 -g data/genomic_data/smiCra1.chrom.sizes > output/liftover/dunnart_enhancer_500bpsummits.bed

bedtools slop -i output/liftover/E10.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E11.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E12.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E13.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E14.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_enhancer_500bpsummits.bed
bedtools slop -i output/liftover/E15.5_enhancer_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_enhancer_500bpsummits.bed

bedtools slop -i output/liftover/E10.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E10.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E11.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E11.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E12.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E12.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E13.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E13.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E14.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E14.5_promoter_500bpsummits.bed
bedtools slop -i output/liftover/E15.5_promoter_summits.bed -b 250 -g data/genomic_data/mm10.chrom.sizes > output/liftover/E15.5_promoter_500bpsummits.bed

LiftOver extended peak summits

LiftOver dunnart peaks to mouse genome


## Enhancer-associated peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10_unmapped.bed

## Promoter-associated peaks
liftOver output/liftover/dunnart_promoter_50bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10.bed output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10_unmapped.bed

Lift back to the dunnart genome

## Enhancer-associated peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

## Promoter-associated peaks
liftOver output/liftover/dunnart_promoter_50bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits_smiCraTOmm10.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_unmapped.bed

Lift back to mouse genome so that everything is in mouse coordinates

## Enhancer-assocaited peaks
liftOver output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

## Promoter-associated peaks 
liftOver output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

liftOver output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10_unmapped.bed

Intersect dunnart CREs with mouse CREs

## Promoter-associated peaks
bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_promoter_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_promoter_500bpsummits.bed

## Enhancer-associated peaks
bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_100bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_200bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_300bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_400bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak -wo > output/liftover/E10.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak -wo > output/liftover/E11.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak -wo > output/liftover/E12.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak -wo > output/liftover/E13.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak -wo > output/liftover/E14.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak -wo > output/liftover/E15.5_mm10intersect_dunnart_enhancer_500bpsummits.bed

Use window to allow intersections within 50 bps

bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E10_cluster1_peaks.narrowPeak  > output/liftover/E10.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E11_cluster1_peaks.narrowPeak  > output/liftover/E11.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E12_cluster1_peaks.narrowPeak  > output/liftover/E12.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E13_cluster1_peaks.narrowPeak  > output/liftover/E13.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E14_cluster1_peaks.narrowPeak  > output/liftover/E14.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_promoter_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/filtered_peaks/E15_cluster1_peaks.narrowPeak  > output/liftover/E15.5_mm10intersect_dunnart_promoter_50bpsummits_window.bed

bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E10.5_enhancer_peaks.narrowPeak  > output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E11.5_enhancer_peaks.narrowPeak  > output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E12.5_enhancer_peaks.narrowPeak  > output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E13.5_enhancer_peaks.narrowPeak  > output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E14.5_enhancer_peaks.narrowPeak  > output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed
bedtools window -w 50 -u -a output/liftover/dunnart_enhancer_50bpsummits.bed_smiCraTOmm10_mm10TOsmiCra_backTOmm10.bed -b output/peaks/E15.5_enhancer_peaks.narrowPeak  > output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed

Lift dunnart peaks back over to the dunnart genome

liftOver -bedPlus=4 output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E10.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E11.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E12.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E13.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E14.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

liftOver -bedPlus=4 output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window.bed output/wga/liftOver_chains/mm10TOsmiCra1_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra.bed output/liftover/E15.5_mm10intersect_dunnart_enhancer_50bpsummits_window_backTOsmiCra_unmapped.bed

When you lift over a peak from one species to another, does it always land next to the same gene in both species?

Use annotated peak files for all peaks and compare nearest gene call

Intersect annotation file with peak summits

bedtools intersect -a output/liftover/dunnart_promoter_50bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_50bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_50bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_50bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_50bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_50bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_50bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_50bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_50bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_50bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_50bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_50bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_50bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_50bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_50bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_50bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_100bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_100bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_100bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_100bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_100bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_100bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_100bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_100bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_100bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_100bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_100bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_100bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_100bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_100bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_100bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_100bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_200bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_200bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_200bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_200bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_200bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_200bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_200bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_200bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_200bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_200bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_200bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_200bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_200bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_200bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_200bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_200bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_300bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_300bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_300bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_300bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_300bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_300bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_300bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_300bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_300bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_300bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_300bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_300bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_300bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_300bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_300bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_300bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_400bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_400bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_400bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_400bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_400bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_400bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_400bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_400bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_400bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_400bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_400bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_400bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_400bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_400bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_400bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_400bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_promoter_500bpsummits.bed -b output/annotations/dunnart_promoter_cluster1_annotationConvertedIDs.bed -wb > output/liftover/dunnart_promoter_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/dunnart_enhancer_500bpsummits.bed -b output/annotations/dunnart_enhancer_annotationConvertedIDs.bed -wb > output/liftover/dunnart_enhancer_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_promoter_500bpsummits.bed -b output/annotations/E10_cluster1_annotation.bed -wb > output/liftover/E10_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_promoter_500bpsummits.bed -b output/annotations/E11_cluster1_annotation.bed -wb > output/liftover/E11_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_promoter_500bpsummits.bed -b output/annotations/E12_cluster1_annotation.bed -wb > output/liftover/E12_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_promoter_500bpsummits.bed -b output/annotations/E13_cluster1_annotation.bed -wb > output/liftover/E13_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_promoter_500bpsummits.bed -b output/annotations/E14_cluster1_annotation.bed -wb > output/liftover/E14_promoter_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_promoter_500bpsummits.bed -b output/annotations/E15_cluster1_annotation.bed -wb > output/liftover/E15_promoter_500bpsummits_annotation.bed

bedtools intersect -a output/liftover/E10.5_enhancer_500bpsummits.bed -b output/annotations/E10.5_enhancer_annotation.bed -wb > output/liftover/E10_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E11.5_enhancer_500bpsummits.bed -b output/annotations/E11.5_enhancer_annotation.bed -wb > output/liftover/E11_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E12.5_enhancer_500bpsummits.bed -b output/annotations/E12.5_enhancer_annotation.bed -wb > output/liftover/E12_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E13.5_enhancer_500bpsummits.bed -b output/annotations/E13.5_enhancer_annotation.bed -wb > output/liftover/E13_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E14.5_enhancer_500bpsummits.bed -b output/annotations/E14.5_enhancer_annotation.bed -wb > output/liftover/E14_enhancer_500bpsummits_annotation.bed
bedtools intersect -a output/liftover/E15.5_enhancer_500bpsummits.bed -b output/annotations/E15.5_enhancer_annotation.bed -wb > output/liftover/E15_enhancer_500bpsummits_annotation.bed

Liftover dunnart peaks with annotation to mouse

liftOver -bedPlus=4 output/liftover/dunnart_promoter_50bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_50bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_100bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_100bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_200bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_200bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_300bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_300bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_400bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_400bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_promoter_500bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_promoter_500bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_50bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_50bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_100bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_100bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_200bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_200bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_300bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_300bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_400bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_400bpsummits_annotation_smiCraTOmm10_unmapped.bed

liftOver -bedPlus=4 output/liftover/dunnart_enhancer_500bpsummits_annotation.bed output/wga/liftOver_chains/smiCra1TOmm10_patched_sorted_repFil_chainCl_preNet_chainNet_stitched.chain output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10.bed output/liftover/dunnart_enhancer_500bpsummits_annotation_smiCraTOmm10_unmapped.bed

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS/LAPACK: /usr/local/easybuild-2019/easybuild/software/compiler/gcc/10.2.0/openblas/0.3.12/lib/libopenblas_haswellp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitr_1.33        data.table_1.14.0 workflowr_1.7.0  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3      highr_0.9         jquerylib_0.1.4   pillar_1.6.1     
 [5] compiler_4.1.0    bslib_0.2.5.1     later_1.2.0       git2r_0.28.0     
 [9] tools_4.1.0       getPass_0.2-2     digest_0.6.27     jsonlite_1.7.2   
[13] evaluate_0.14     lifecycle_1.0.1   tibble_3.1.2      pkgconfig_2.0.3  
[17] rlang_1.0.2       cli_2.5.0         rstudioapi_0.13   yaml_2.2.1       
[21] xfun_0.23         httr_1.4.2        stringr_1.4.0     sass_0.4.0       
[25] fs_1.5.0          vctrs_0.3.8       rprojroot_2.0.2   glue_1.4.2       
[29] R6_2.5.0          processx_3.5.2    fansi_0.5.0       rmarkdown_2.8    
[33] callr_3.7.0       magrittr_2.0.1    whisker_0.4       ps_1.6.0         
[37] promises_1.2.0.1  ellipsis_0.3.2    htmltools_0.5.1.1 httpuv_1.6.1     
[41] utf8_1.2.1        stringi_1.6.2     crayon_1.4.1

Cross-species peak level comparisons

lecook

2022-02-23