Chapter 2 Validation-deeptools-heatmap
2.1 Description
check the definition for lineage-conserved and lineage-specific CBSs by deeptools
2.2 Input data
data/DiffBD/human-LiverVSAllother-CTCF.diffBD.minOverlap1.log2FC1FDR0001.upinLiver.D210112-Alltissues.bed
data/DiffBD/human-MTVSAllotherWithouMB-CTCF.diffBD.minOverlap1.log2FC1FDR001.upinMT.D210112-Alltissues.bed
data/DiffBD/human-BcellVSAllotherWithoutNeutrophilANDmonocyteE-CTCF.diffBD.minOverlap1.log2FC1FDR005.upinBcell.D210112-Alltissues.bed
data/DiffBD/liver.npc.mt.macrophage.mb.lungfibroblast.spleen.netrophil.center400bp.bed
2.3 Process
- compute matrix
# shuf-conserved and specific CBS
bw="../../../../public-chip/Human-TFandhist/CTCF/align/E-MTAB-437-Human-Liver-CTCF-treat/E-MTAB-437-Human-Liver-CTCF-treat.MAPQ30.merge.bam.RPKM.bw ../../../../public-chip/Human-TFandhist/CTCF/align/GSE128527-CTCF-human-MT-treat/GSE128527-CTCF-human-MT-treat.MAPQ30.merge.bam.RPKM.bw ../../../../public-chip/Human-TFandhist/CTCF/align/ENCSR000AUV-human-Bcell-CTCF/ENCSR000AUV-human-Bcell-CTCF.MAPQ30.merge.bam.RPKM.bw"
pkurun computeMatrix reference-point -S $bw -R ../regions/CTCF/liver.npc.mt.macrophage.mb.lungfibroblast.spleen.netrophil.shuf5k.bed ../regions/CTCF/human-LiverVSAllother-CTCF.diffBD.minOverlap1.log2FC1FDR0001.upinLiver.D210112-Alltissues.bed ../regions/CTCF/human-MTVSAllotherWithouMB-CTCF.diffBD.minOverlap1.log2FC1FDR001.upinMT.D210112-Alltissues.bed ../regions/CTCF/human-BcellVSAllotherWithoutNeutrophilANDmonocyteE-CTCF.diffBD.minOverlap1.log2FC1FDR005.upinBcell.D210112-Alltissues.bed -a 1500 -b 1500 --referencePoint center --samplesLabel Hepatocyte Myocyte Bcell -p 20 -o Hep.MT.Bcell.CTCF_ON_stableshuf5kCBS_diffBDCBS_matrix.gz
# all-conserved CBS
pkurun computeMatrix reference-point -S $bw -R ../regions/CTCF/liver.npc.mt.macrophage.mb.lungfibroblast.spleen.netrophil -a 1500 -b 1500 --referencePoint center --samplesLabel Hepatocyte Myocyte Bcell -p 20 -o Hep.MT.Bcell.CTCF_ON_stableCBS_matrix.gz
# specific CBS
pkurun computeMatrix reference-point -S $bw -R ../regions/CTCF/human-LiverVSAllother-CTCF.diffBD.minOverlap1.log2FC1FDR0001.upinLiver.D210112-Alltissues.bed ../regions/CTCF/human-MTVSAllotherWithouMB-CTCF.diffBD.minOverlap1.log2FC1FDR001.upinMT.D210112-Alltissues.bed ../regions/CTCF/human-BcellVSAllotherWithoutNeutrophilANDmonocyteE-CTCF.diffBD.minOverlap1.log2FC1FDR005.upinBcell.D210112-Alltissues.bed -a 1500 -b 1500 --referencePoint center --samplesLabel Hepatocyte Myocyte Bcell -p 20 -o Hep.MT.Bcell.CTCF_ON_diffBDCBS_matrix.gz
- plot heatmap and profile
plotProfile -m /lustre1/lch3000_pkuhpc/liuyt/ChenQ/Figures-D2106/Deeptools/Fig1-CTCF-Enh-Hg/results/Hep.MT.Bcell.CTCF_ON_diffBDCBS_matrix.gz -o Hep.MT.Bcell.CTCF_ON_diffBDCBS_matrix.gz_plotprofile.pdf -z hep-s myo-s bcell-s --perGroup --plotHeight 4 --plotWidth 4
plotHeatmap -m /lustre1/lch3000_pkuhpc/liuyt/ChenQ/Figures-D2106/Deeptools/Fig1-CTCF-Enh-Hg/results/Hep.MT.Bcell.CTCF_ON_diffBDCBS_matrix.gz -o Hep.MT.Bcell.CTCF_ON_diffBDCBS_matrix.gz_plotheatmap.pdf --colorMap Oranges Blues Greens --heatmapHeight 4.5 --heatmapWidth 1 --whatToShow "heatmap and colorbar" -z hep-s myo-s bcell-s
2.4 Output
- results/Validation/Hep.MT.Bcell.CTCF_ON*