/
HistoneModandPAS.Rmd
384 lines (249 loc) · 15.2 KB
/
HistoneModandPAS.Rmd
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---
title: "Chromatin marks and PAS"
author: "Briana Mittleman"
date: "3/20/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
http://science.sciencemag.org/content/352/6291/aad9926.full?ijkey=fkp/DIzVNS9RY&keytype=ref&siteid=sci
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
Deeptools plot
h3k27me3DTmypeaks.sh
```{bash,eval=F}
#!/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.png
```
Put 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
```{bash,eval=F}
#!/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 -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
```
Scales are too different to put these on the same spot:
H3k27me3DTmyPAS.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=H3k27me3DTmypeaks.sh
#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/MergedGm06990H3k27me3.bw -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 5000 -a 5000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k27me3_myPeaksNompfilt.gz --outFileNameMatrix /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k27me3_myPeaksNompfilt_matrix.txt --outFileSortedRegions /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k27me3_myPeaksNompfilt_SortedRegions.txt
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.png
```
H3k36me3DTmyPAS.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=H3k27me3DTmypeaks.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3k36me3DTmypeaks.out
#SBATCH --error=H3k36me3DTmypeaks.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/MergedGm06990H3k36me3.bw -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 5000 -a 5000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k36me3_myPeaksNompfilt.gz --outFileNameMatrix /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k36me3_myPeaksNompfilt_matrix.txt --outFileSortedRegions /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k36me3_myPeaksNompfilt_SortedRegions.txt
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k36me3_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "H3k36me3 at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k36me3_myPeaksNompfilt.png
```
H3k4me3DTmyPAS.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=H3k4me3DTmypeaks.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3k36me3DTmypeaks.out
#SBATCH --error=H3k36me3DTmypeaks.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/MergedGm06990H3k4me3.bw -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 5000 -a 5000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k4me3_myPeaksNompfilt.gz --outFileNameMatrix project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k4me3_myPeaksNompfilt_matrix.txt --outFileSortedRegions /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k4me3_myPeaksNompfilt_SortedRegions.txt
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k4me3_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "H3k4me3 at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/H3k4me3_myPeaksNompfilt.png
```
##Download both replicates for these and merge:
mergeH3k27me3.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=mergeH3k27me3
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeH3k27me3.out
#SBATCH --error=mergeH3k27me3.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
bigWigMerge /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k27me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k27me3StdRawRep2.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k27me3.bedGraph
sort -k1,1 -k2,2n /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k27me3.bedGraph /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k27me3.sort.bedGraph
bedGraphToBigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k27me3.sort.bedGraph /project2/gilad/briana/genome_anotation_data/chrom.length.chr.txt /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k27me3.bw
```
mergeH3k36me3.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=mergeH3k36me3
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeH3k36me3.out
#SBATCH --error=mergeH3k36me3.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
bigWigMerge /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k36me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k36me3StdRawRep2.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k36me3.bedGraph
sort -k1,1 -k2,2n /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k36me3.bedGraph > /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k36me3.sort.bedGraph
bedGraphToBigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k36me3.sort.bedGraph /project2/gilad/briana/genome_anotation_data/chrom.length.chr.txt /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k36me3.bw
```
mergeH3k4me3.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=mergeH3k4me3
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeH3k4me3.out
#SBATCH --error=mergeH3k4me3.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
bigWigMerge /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k4me3StdRawRep1.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/wgEncodeUwHistoneGm06990H3k4me3StdRawRep2.bigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k4me3.bedGraph
sort -k1,1 -k2,2n /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k4me3.bedGraph >/project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k4me3.sort.bedGraph
bedGraphToBigWig /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k4me3.sort.bedGraph /project2/gilad/briana/genome_anotation_data/chrom.length.chr.txt /project2/gilad/briana/threeprimeseq/data/ChipSeq/MergedGm06990H3k4me3.bw
```
##MNASE:
MNASEmyPAS.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=MNASEmyPAS
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=MNASEmyPAS.out
#SBATCH --error=MNASEmyPAS.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/ENCFF000VME.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "MNASE at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNompfilt.png
```
Try second mnase track.
MNASEmyPAS_secondfile.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=MNASEmyPAS_secondfile
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=MNASEmyPAS_secondfile.out
#SBATCH --error=MNASEmyPAS_secondfile.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/wgEncodeSydhNsomeGm12878Sig.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase2_myPeaksNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase2_myPeaksNompfilt.gz --refPointLabel "Called PAS" --plotTitle "MNASE at All Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase2_myPeaksNompfilt.png
```
Convert to PAS ratehr than peak:
APAPeaks_5percCov_fixedStrand_INTRON.bed
```{bash,eval=F}
python Peak2PAS.py /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPeaks_5percCov_fixedStrand_INTRON.bed /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_INTRON.bed
```
Run this with intronic vs utr
MNASEmyPASIntron.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=MNASEmyPASIntron
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=MNASEmyPASIntron.out
#SBATCH --error=MNASEmyPASIntron.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/ENCFF000VME.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_INTRON.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksIntronNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksIntronNompfilt.gz --refPointLabel "Called PAS" --plotTitle "MNASE at Intronic Called PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksIntronNompfilt.png
```
Nuclear specific:
```{bash,eval=F}
python Peak2PAS.py /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPeaks_5percCov_fixedStrand_SigUsageNuc.bed /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_SigUsageNuc.bed
```
MNASEmyPASNuclear.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=MNASEmyPASNuclear
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=MNASEmyPASNuclear.out
#SBATCH --error=MNASEmyPASNuclear.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/ENCFF000VME.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_SigUsageNuc.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearNompfilt.gz --refPointLabel "Called PAS" --plotTitle "MNASE at Nuclear specific PAS" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearNompfilt.png
```
Nuclear Intronic:
APAPeaks_5percCov_fixedStrand_SigUsageNuc_Intron.bed
```{bash,eval=F}
python Peak2PAS.py /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPeaks_5percCov_fixedStrand_SigUsageNuc_Intron.bed /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_SigUsageNuc_Intron.bed
```
MNASEmyPASNuclearIntronic.sh
```{bash,eval=F}
#!/bin/bash
#SBATCH --job-name=MNASEmyPASNuclearIntronic
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=MNASEmyPASNuclearIntronic.out
#SBATCH --error=MNASEmyPASNuclearIntronic.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/ENCFF000VME.bigWig -R /project2/gilad/briana/threeprimeseq/data/peaks4DT/APAPAS_5percCov_fixedStrand_SigUsageNuc_Intron.bed -b 1000 -a 1000 -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearIntronNompfilt.gz
plotHeatmap --sortRegions descend -m /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearIntronNompfilt.gz --refPointLabel "Called PAS" --plotTitle "MNASE at Nuclear specific PAS in Intron" --heatmapHeight 7 --colorMap YlGnBu -out /project2/gilad/briana/threeprimeseq/data/ChipSeq/mnase_myPeaksNuclearIntronNompfilt.png
```