Last updated: 2019-01-10
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Unstaged changes:
Modified: analysis/28ind.peak.explore.Rmd
Modified: analysis/CompareLianoglouData.Rmd
Modified: analysis/InvestigatePeak2GeneAssignment.Rmd
Modified: analysis/apaQTLoverlapGWAS.Rmd
Modified: analysis/cleanupdtseq.internalpriming.Rmd
Modified: analysis/coloc_apaQTLs_protQTLs.Rmd
Modified: analysis/dif.iso.usage.leafcutter.Rmd
Modified: analysis/diff_iso_pipeline.Rmd
Modified: analysis/explainpQTLs.Rmd
Modified: analysis/explore.filters.Rmd
Modified: analysis/flash2mash.Rmd
Modified: analysis/overlapMolQTL.Rmd
Modified: analysis/overlap_qtls.Rmd
Modified: analysis/peakOverlap_oppstrand.Rmd
Modified: analysis/pheno.leaf.comb.Rmd
Modified: analysis/swarmPlots_QTLs.Rmd
Modified: analysis/test.max2.Rmd
Modified: analysis/understandPeaks.Rmd
Modified: code/Snakefile
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.
I want to use this analysis to create reproduciple genome track figures. I will use the python package pygenometracks.
#Give a bed or bw
make_tracks_file --trackFiles <file1.bed> <file2.bw> ... -o tracks.ini
pyGenomeTracks --tracks tracks.ini --region chr2:10,000,000-11,000,000 --outFileName nice_image.pdf
Try this with 1 individual.
#make_tracks_file --trackFiles /project2/gilad/briana/threeprimeseq/data/bed/YL-SP-19257-T-combined.bed /project2/gilad/briana/threeprimeseq/data/bed/YL-SP-19257-N-combined.bed /project2/gilad/briana/genome_anotation_data/refseq.ProteinCoding.bed -o /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.tracks.ini
#pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.tracks.ini --region chr7:5,564,986-5,572,554 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/actb_19257.png
#make with bigwig
make_tracks_file --trackFiles /project2/gilad/briana/threeprimeseq/data/bigwig/YL-SP-19257-T-combined.bw /project2/gilad/briana/threeprimeseq/data/bigwig/YL-SP-19257-N-combined.bw /project2/gilad/briana/genome_anotation_data/NCBI_refseq_forPyGenTrack_sort.bed -o /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.BW.tracks.ini
/project2/gilad/briana/threeprimeseq/data/bigwig/YL-SP-19257-N-combined.bw
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.BW.tracks.ini --region chr7:5,564,986-5,572,554 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/actb_19257.png
I can also add a track with the peaks!cd . /project2/gilad/briana/threeprimeseq/data/mergedPeaks_comb/filtered_APApeaks_merged_allchrom_refseqTrans.noties_sm.fixed.bed
awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" "1" "\t" $6}' /project2/gilad/briana/genome_anotation_data/ncbiRefSeq_endProtCodGenes_sort.bed | head
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.BW.tracks.ini --region chr1:1,680,671-1,713,508 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/nadk_19257_BW.png
#gata3 chr10:8,094,667-8,119,164
#try all ind.
make_tracks_file --trackFiles /project2/gilad/briana/threeprimeseq/data/bigwig/*combined.bw /project2/gilad/briana/genome_anotation_data/NCBI_refseq_forPyGenTrack_sort.bed -o /project2/gilad/briana/threeprimeseq/data/genome_tracks/allInd.BW.tracks.ini
I want to make this with 1 individal and the corresponding RNA seq track.
First I need to make a BW file for the RNA seq.
NA19257RNAseq2bw.sh
#!/bin/bash
#SBATCH --job-name=NA19257RNAseq2bw
#SBATCH --account=pi-yangili1
#SBATCH --time=36:00:00
#SBATCH --output=NA19257RNAseq2bw.out
#SBATCH --error=NA19257RNAseq2bw.err
#SBATCH --partition=broadwl
#SBATCH --mem=30G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
bedtools genomecov -ibam /project2/yangili1/LCL/RNAseqGeuvadisBams/RNAseqGeuvadis_STAR_19257.final.bam -bg -split > /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.bg
sort -k1,1 -k2,2n /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.bg > /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.sort.bg
bedGraphToBigWig /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.sort.bg /project2/gilad/briana/genome_anotation_data/chrom.length.txt /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.sort.bw
make_tracks_file --trackFiles /project2/gilad/briana/threeprimeseq/data/bigwig/YL-SP-19257-T-combined.bw /project2/gilad/briana/threeprimeseq/data/bigwig/YL-SP-19257-N-combined.bw /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_19257.final.sort.bw /project2/gilad/briana/genome_anotation_data/NCBI_refseq_forPyGenTrack_sort.bed -o /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.RNA.BW.tracks.ini
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/NA19257.RNA.BW.tracks.ini --region chr17:27900300-27916800 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/git1_19257_rna_BW.png
Zoom into UTR for all individuals to show replicability
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/allInd.BW.tracks.ini --region chr17:27900300-27902000 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/git1_allind_UTR_BW_.png
make_tracks_file --trackFiles /project2/gilad/briana/threeprimeseq/data/mergedBW/Total_MergedBamCoverage.bw /project2/gilad/briana/threeprimeseq/data/mergedBW/Nuclear_MergedBamCoverage.bw /project2/gilad/briana/threeprimeseq/data/rnaseq_bw/RNAseqGeuvadis_STAR_6samp_MergedBams.sort.bw /project2/gilad/briana/genome_anotation_data/NCBI_refseq_forPyGenTrack_sort.bed -o /project2/gilad/briana/threeprimeseq/data/genome_tracks/MergedBW.RNA.BW.tracks.ini
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/MergedBW.RNA.BW.tracks.ini --region chr17:27900300-27916800 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/git1_MergedBW_rna_BW.png
zoom in with this one:
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/MergedBW.RNA.BW.tracks.ini --region chr17:27900300-27902000 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/git1_UTR_MergedBW_rna_BW.png
Specificity plot? RNA without 3’
pyGenomeTracks --tracks /project2/gilad/briana/threeprimeseq/data/genome_tracks/MergedBW.RNA.BW.tracks.ini --region chr3:169482033-169483209 --outFileName /project2/gilad/briana/threeprimeseq/data/genome_tracks/terc_MergedBW_rna_BW.png
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.19 digest_0.6.17
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] stringi_1.2.4 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.7.0 rmarkdown_1.10 tools_3.5.1
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.5.1
[19] htmltools_0.3.6 knitr_1.20
This reproducible R Markdown analysis was created with workflowr 1.1.1