Genome Tracks with pyGenomeTracks

Last updated: 2019-01-10

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Ignored files:
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    Ignored:    data/.DS_Store
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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

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File	Version	Author	Date	Message
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.

Add to Conda environment (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

merged bam file


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

Session information

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

Genome Tracks with pyGenomeTracks

Briana Mittleman

10/1/2018

merged bam file

Session information