Delete deeptools_analysis directory (9299177d) · Commits · Chaos / 3D_chromatin_in_AML

deeptools_analysis/README.md

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		## deeptools analysis for ChIPseq and ATACseq differetnial peaks
		deeptools_ChIPseq_ATACseq.R


		## deeptools analysis for peaks showing leukemia-specific changes
		deeptools_leukemia_specific_changes.R

		## deeptools analysis for 10 tsne clusters from Seurat-guided intergrative anlaysis
		deeptools_tsne_clusters.R

deeptools_analysis/deeptools_ChIPseq_ATACseq.R

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		### deeptools heatmap and profile plots

		## ATAC
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R WD.ATAC.up_summit500.bed WD.ATAC.down_summit500.bed -S LN.ATAC.R1-2.cpm_peaks.bw NPM1.ATAC.R1-2.cpm_peaks.bw FLT3.ATAC.R1-2.cpm_peaks.bw DM.ATAC.R1-2.cpm_peaks.bw -o WNFD_ATAC.gz --missingDataAsZero -p 12

		plotHeatmap -m WNFD_ATAC.gz -out WNFD_ATAC_heatmap.pdf --colorMap Greens --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel 'Accessibility gain in DM' 'Accessibility loss in DM' --refPointLabel 'center' --legendLocation 'none' --whatToShow 'heatmap and colorbar'

		plotProfile -m WNFD_ATAC.gz -out WNFD_ATAC_profile.pdf --perGroup --numPlotsPerRow 1 --plotWidth 7.25 --plotHeight 6.5 --dpi 300 --refPointLabel 'center' --legendLocation 'upper-left' --plotType 'se' -y 'ATAC-seq enrichment' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --samplesLabel 'WT' 'NPM1' 'FLT3' 'DM' --regionsLabel 'Accessibility gain in DM' 'Accessibility loss in DM'

		### H3K4me1
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC.summit_ov.WD.H3K4me1.up.bed ATAC.summit_ov.WD.H3K4me1.down.bed -S LN.H3K4me1.R1-2.cpm_peaks.bw NPM1.H3K4me1.R1-2.cpm_peaks.bw FLT3.H3K4me1.R1-2.cpm_peaks.bw DM.H3K4me1.R1-2.cpm_peaks.bw -o WNFD_H3K4me1.gz --missingDataAsZero -p 16

		plotHeatmap -m WNFD_H3K4me1.gz -out WNFD_H3K4me1_heatmap.pdf --colorMap Oranges --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel 'H3K4me1 gain in DM' 'H3K4me1 loss in DM' --refPointLabel 'center' --legendLocation 'none' --whatToShow 'heatmap and colorbar'

		plotProfile -m WNFD_H3K4me1.gz -out WNFD_H3K4me1_profile.pdf --perGroup --numPlotsPerRow 1 --plotWidth 7.25 --plotHeight 6.5 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' --yMin 0 0 --yMax 4 4 -y 'H3K4me1 enrichment' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --regionsLabel 'H3K4me1 gain in DM' 'H3K4me1 loss in DM'

		### H3K27ac
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC.summit_ov.WD.H3K27ac.up.bed ATAC.summit_ov.WD.H3K27ac.down.bed -S LN.H3K27ac.R1-2.cpm_peaks.bw NPM1.H3K27ac.R1-2.cpm_peaks.bw FLT3.H3K27ac.R1-2.cpm_peaks.bw DM.H3K27ac.R1-2.cpm_peaks.bw -o WNFD_H3K27ac.gz --missingDataAsZero -p 16

		plotHeatmap -m WNFD_H3K27ac.gz -out WNFD_H3K27ac_heatmap.pdf --colorMap Purples --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel 'H3K27ac gain in DM' 'H3K27ac loss in DM' --refPointLabel 'center' --legendLocation 'none' --whatToShow 'heatmap and colorbar'

		plotProfile -m WNFD_H3K27ac.gz -out WNFD_H3K27ac_profile.pdf --perGroup --numPlotsPerRow 1 --plotWidth 7.25 --plotHeight 6.5 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' --yMin 0 0 --yMax 14 14 -y 'H3K27ac enrichment' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --regionsLabel 'H3K27ac gain in DM' 'H3K27ac loss in DM'

deeptools_analysis/deeptools_leukemia_specific_changes.R

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		### analyse leukemia specific changes with deeptools
		## up
		## creat 2-clusters with NE profile only
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R atac_co20.summit200bp.ov.WD.enh.H3K4me1.up.bed -S NE.H3K4me1.cpm.bw -o atac_summit.ov.WD.enh.up_Ne.H3K4me1.gz --missingDataAsZero -p 8

		plotHeatmap -m atac_summit.ov.WD.enh.up_Ne.H3K4me1.gz -out atac_summit.ov.WD.enh.up_Ne.H3K4me1.2cluster_heatmap.pdf --colorMap coolwarm --samplesLabel 'NE' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel '1' '2' --refPointLabel 'center' --legendLocation 'none' --outFileSortedRegions atac_summit.ov.Ne.enh.up_H3K4me1.2cluster.bed --kmeans 2 --whatToShow 'heatmap and colorbar'

		sort -k1,1 -k2,2n atac_summit.ov.Ne.enh.up_H3K4me1.2cluster.bed \| awk '{if ($13 == "1") print $1"\t"$2"\t"$3}' > Ne.up_WDNG_k4me1.cluster1.bed
		sort -k1,1 -k2,2n atac_summit.ov.Ne.enh.up_H3K4me1.2cluster.bed \| awk '{if ($13 == "2") print $1"\t"$2"\t"$3}' > Ne.up_WDNG_k4me1.cluster2.bed

		### down
		## creat 2-clusters with NE profile only
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R atac_co20.summit200bp.ov.WD.enh.H3K4me1.down.bed -S NE.H3K4me1.cpm.bw -o atac_summit.ov.WD.enh.down_Ne.H3K4me1.gz --missingDataAsZero -p 18

		plotHeatmap -m atac_summit.ov.WD.enh.down_Ne.H3K4me1.gz -out atac_summit.ov.WD.enh.down_Ne.H3K4me1.2cluster_heatmap.pdf --colorMap coolwarm --samplesLabel 'NE' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel '3' '4' --refPointLabel 'center' --legendLocation 'none' --outFileSortedRegions atac_summit.ov.Ne.enh.down_H3K4me1.2cluster.bed --kmeans 2 --whatToShow 'heatmap and colorbar'

		sort -k1,1 -k2,2n atac_summit.ov.Ne.enh.down_H3K4me1.2cluster.bed \| awk '{if ($13 == "3") print $1"\t"$2"\t"$3}' > Ne.down_WDNG_k4me1.cluster3.bed
		sort -k1,1 -k2,2n atac_summit.ov.Ne.enh.down_H3K4me1.2cluster.bed \| awk '{if ($13 == "4") print $1"\t"$2"\t"$3}' > Ne.down_WDNG_k4me1.cluster4.bed

		### combined plots
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R Ne.up_WDNG_k4me1.cluster1.bed Ne.up_WDNG_k4me1.cluster2.bed Ne.down_WDNG_k4me1.cluster3.bed Ne.down_WDNG_k4me1.cluster4.bed -S LN.H3K4me1.cpm.bw DM.H3K4me1.cpm.bw NE.H3K4me1.cpm.bw GMP.K4ME1.re.cpm_peaks_norm.bw LN.H3K27ac.cpm.bw DM.H3K27ac.cpm.bw NE.H3K27ac.cpm.bw GMP.H3K27AC.re.cpm_peaks_norm.bw LN.ATAC.cpm_peaks.bw DM.ATAC.cpm_peaks.bw NE.ATAC.cpm_peaks.bw GMP.ATAC_NEW.cpm_peaks.bw -o WDNG_all.gz --missingDataAsZero -p 20

		plotHeatmap -m WDNG_all.gz -out WDNG_all_sortbyall_heatmap.pdf --colorMap Oranges Oranges Oranges Oranges Purples Purples Purples Purples Greens Greens Greens Greens --samplesLabel 'WT' 'DM' 'NEU' 'GMP' 'WT' 'DM' 'NEU' 'GMP' 'WT' 'DM' 'NEU' 'GMP' --heatmapHeight 10 --heatmapWidth 1.5 --dpi 300 -x '' --regionsLabel 'Gain-1' 'Gain-2' 'Loss-1' 'Loss-2' --zMin 0 0 0 0 0 0 0 0 0 0 0 0 --zMax 2.2 2.2 2.2 2.2 2.5 2.5 2.5 2.5 12 12 12 12 --refPointLabel 'center' --legendLocation 'none' --whatToShow 'heatmap and colorbar'

deeptools_analysis/deeptools_tsne_clusters.R

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		### deeptools for tsne clusters
		# H3K4me1
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC_consensus_summit2kb_tsne.cluster-1.bed ATAC_consensus_summit2kb_tsne.cluster-2.bed ATAC_consensus_summit2kb_tsne.cluster-3.bed ATAC_consensus_summit2kb_tsne.cluster-4.bed ATAC_consensus_summit2kb_tsne.cluster-5.bed ATAC_consensus_summit2kb_tsne.cluster-6.bed ATAC_consensus_summit2kb_tsne.cluster-7.bed ATAC_consensus_summit2kb_tsne.cluster-8.bed ATAC_consensus_summit2kb_tsne.cluster-9.bed ATAC_consensus_summit2kb_tsne.cluster-10.bed -S LN.H3K4me1.R1-2.cpm_peaks.bw NPM1.H3K4me1.R1-2.cpm_peaks.bw FLT3.H3K4me1.R1-2.cpm_peaks.bw DM.H3K4me1.R1-2.cpm_peaks.bw -o TSNE_10clusters_H3K4me1.gz --missingDataAsZero -p 18

		plotProfile -m TSNE_10clusters_H3K4me1.gz -out TSNE_10clusters_H3K4me1_profile.pdf --perGroup --numPlotsPerRow 10 --plotWidth 3.59 --plotHeight 4.72 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' -y 'H3K4me1' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --regionsLabel '1' '2' '3' '4' '5' '6' '7' '8' '9' '10'

		# H3K4me3
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC_consensus_summit2kb_tsne.cluster-1.bed ATAC_consensus_summit2kb_tsne.cluster-2.bed ATAC_consensus_summit2kb_tsne.cluster-3.bed ATAC_consensus_summit2kb_tsne.cluster-4.bed ATAC_consensus_summit2kb_tsne.cluster-5.bed ATAC_consensus_summit2kb_tsne.cluster-6.bed ATAC_consensus_summit2kb_tsne.cluster-7.bed ATAC_consensus_summit2kb_tsne.cluster-8.bed ATAC_consensus_summit2kb_tsne.cluster-9.bed ATAC_consensus_summit2kb_tsne.cluster-10.bed -S LN.H3K4me3.R1-2.cpm_peaks.bw NPM1.H3K4me3.R1-2.cpm_peaks.bw FLT3.H3K4me3.R1-2.cpm_peaks.bw DM.H3K4me3.R1-2.cpm_peaks.bw -o TSNE_10clusters_H3K4me3.gz --missingDataAsZero -p 18

		plotProfile -m TSNE_10clusters_H3K4me3.gz -out TSNE_10clusters_H3K4me3_profile.pdf --perGroup --numPlotsPerRow 10 --plotWidth 4 --plotHeight 5 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' -y 'H3K4me3' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --regionsLabel '1' '2' '3' '4' '5' '6' '7' '8' '9' '10'

		# H3K27ac
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC_consensus_summit2kb_tsne.cluster-1.bed ATAC_consensus_summit2kb_tsne.cluster-2.bed ATAC_consensus_summit2kb_tsne.cluster-3.bed ATAC_consensus_summit2kb_tsne.cluster-4.bed ATAC_consensus_summit2kb_tsne.cluster-5.bed ATAC_consensus_summit2kb_tsne.cluster-6.bed ATAC_consensus_summit2kb_tsne.cluster-7.bed ATAC_consensus_summit2kb_tsne.cluster-8.bed ATAC_consensus_summit2kb_tsne.cluster-9.bed ATAC_consensus_summit2kb_tsne.cluster-10.bed -S LN.H3K27ac.R1-2.cpm_peaks.bw NPM1.H3K27ac.R1-2.cpm_peaks.bw FLT3.H3K27ac.R1-2.cpm_peaks.bw DM.H3K27ac.R1-2.cpm_peaks.bw -o TSNE_10clusters_H3K27ac.gz --missingDataAsZero -p 18

		plotProfile -m TSNE_10clusters_H3K27ac.gz -out TSNE_10clusters_H3K27ac_profile.pdf --perGroup --numPlotsPerRow 10 --plotWidth 4 --plotHeight 5 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' -y 'H3K27ac' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --regionsLabel '1' '2' '3' '4' '5' '6' '7' '8' '9' '10'

		# ATAC-seq
		computeMatrix reference-point --referencePoint center -b 1000 -a 1000 -R ATAC_consensus_summit2kb_tsne.cluster-1.bed ATAC_consensus_summit2kb_tsne.cluster-2.bed ATAC_consensus_summit2kb_tsne.cluster-3.bed ATAC_consensus_summit2kb_tsne.cluster-4.bed ATAC_consensus_summit2kb_tsne.cluster-5.bed ATAC_consensus_summit2kb_tsne.cluster-6.bed ATAC_consensus_summit2kb_tsne.cluster-7.bed ATAC_consensus_summit2kb_tsne.cluster-8.bed ATAC_consensus_summit2kb_tsne.cluster-9.bed ATAC_consensus_summit2kb_tsne.cluster-10.bed -S LN.ATAC.R1-2.cpm_peaks.bw NPM1.ATAC.R1-2.cpm_peaks.bw FLT3.ATAC.R1-2.cpm_peaks.bw DM.ATAC.R1-2.cpm_peaks.bw -o TSNE_10clusters_ATAC-seq.gz --missingDataAsZero -p 18

		plotProfile -m TSNE_10clusters_ATAC-seq.gz -out TSNE_10clusters_ATAC-seq_profile.pdf --perGroup --numPlotsPerRow 10 --plotWidth 4 --plotHeight 5 --dpi 300 --refPointLabel 'center' --plotType 'se' --legendLocation 'upper-left' -y 'ATAC-seq' --samplesLabel 'WT' 'Npm1c' 'Flt3-ITD' 'DM' --colors '#AAA9AD' '#0078D7' '#3CAEA3' '#ED553B' --regionsLabel '1' '2' '3' '4' '5' '6' '7' '8' '9' '10'

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