Last updated: 2019-03-20
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Knit directory: threeprimeseq/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 54168fd | Briana Mittleman | 2019-03-20 | add histone mod analysis |
This article talks about chromatin modifications for heterochromatin downstream of PAS. I will look at enrichment for repressive histone marks downstream of my called PAS.
Repressive marks H3K27me3, H3K9me3
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwHistone/
H3k27me3 H3k36me3 H3k4me3 H3k36me3
Deeptools plot
h3k27me3DTmypeaks.sh
#!/bin/bash
#SBATCH --job-name=h3k27me3DTmypeaks
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=h3k27me3DTmypeaks.out
#SBATCH --error=h3k27me3DTmypeaks.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
computeMatrix reference-point -S /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k27me3StdRawRep1.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPeaks_5percCov_fixedStrand.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3K27me3_myPeaksNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3K27me3_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "H3K27me3 at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3K27me3_myPeaksNompfilt.pngPut all of the marks on one plot:
I also want to just use the last base of the peak APAPAS_5percCov_fixedStrand.bed histonemarksDTmypeaks.sh
#!/bin/bash
#SBATCH --job-name=histonemarksDTmypeaks
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=histonemarksDTmypeaks.out
#SBATCH --error=histonemarksDTmypeaks.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
computeMatrix reference-point -S /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k27me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k36me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k4me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm12878H3k36me3StdRawRep1.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/HistMarks_myPeaksNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/HistMarks_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "Histone marks at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/HistMarks_myPeaksNompfilt.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
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