Chapter 8 Histone ChIP-Seq profiles deeptools

8.1 Description

explore the histone modificaiton of k27ac around lineage-conserved and lineage-specific CBSs by deeptools

8.2 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

8.3 Process

  • compute matrix
# shuf-conserved and specific CBS
bw="/lustre1/lch3000_pkuhpc/liuyt/ChenQ/public-chip/Human-TFandhist/histone-H3K27ac/align/ENCSR981UJA-human-rightlobeLiver-tissue-H3K27ac/ENCSR981UJA-human-rightlobeLiver-tissue-H3K27ac.MAPQ30.merge.bam.RPKM.bw /lustre1/lch3000_pkuhpc/liuyt/ChenQ/public-chip/Human-TFandhist/histone-H3K27ac/align/GSM733666-H3K27ac-human-MT-treat/GSM733666-H3K27ac-human-MT-treat.MAPQ30.merge.bam.RPKM.bw /lustre1/lch3000_pkuhpc/liuyt/ChenQ/public-chip/Human-TFandhist/histone-H3K27ac/align/ENCSR000AUP-human-Bcell-H3K27ac/ENCSR000AUP-human-Bcell-H3K27ac.MAPQ30.merge.bam.RPKM.bw"
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.K27ac_ON_stableshuf5kCBS_diffBDCBS_matrix.g

# all-conserved CBS
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.K27ac_ON_stableCBS_matrix.gz
# specific CBS
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.K27ac_ON_diffBDCBS_matrix.gz

8.4 Output

  • results/Features/N8-histone-deeptools/Hep.MT.Bcell.K27ac_ON*