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*