Last updated: 2019-02-15
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Knit directory: threeprimeseq/analysis/
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These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote
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File | Version | Author | Date | Message |
---|---|---|---|---|
html | 0eabb61 | Briana Mittleman | 2019-01-10 | Build site. |
Rmd | 33b4047 | Briana Mittleman | 2019-01-10 | make plots with merged BW |
html | d01545f | Briana Mittleman | 2018-10-30 | Build site. |
Rmd | 9c9486d | Briana Mittleman | 2018-10-30 | add genoem tracks code |
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_1.2.0 Rcpp_0.12.19 digest_0.6.17 rprojroot_1.3-2
[5] backports_1.1.2 git2r_0.24.0 magrittr_1.5 evaluate_0.13
[9] stringi_1.2.4 fs_1.2.6 whisker_0.3-2 rmarkdown_1.11
[13] tools_3.5.1 stringr_1.4.0 glue_1.3.0 yaml_2.2.0
[17] compiler_3.5.1 htmltools_0.3.6 knitr_1.20