Chapter 12 HiC CBS Density around Boundary Calculate

12.1 description

compare the CTCF binding site density distribution for mouse lineage-stable and specific CBS sets; around 1Mb regions centered from boundaries called by diamond insulation methods per celltypes

12.2 input data

  • data/DiffBD/*center400bp.bed
  • data/DiffBD/res-20210322-AllCells-bw/*bw
  • data/HiC/diamond-insulaiton/*filter-0.1.bed

12.3 processing

  • calculate the CBSs distribution
pkurun  computeMatrix reference-point -S Mouse-multipleCells-stable-CBS.center400bp.bed.bw Mouse-HepatocytevsAllotherWithoutENOCDELiverdiffBD.minOverlap1.log2FC1FDR001.upinHepatocyte.center400bp.bed.bw Mouse-MTvsAllotherdiffBD.minOverlap1.log2FC1FDR001.upinMT.center400bp.bed.bw Mouse-SplenicBcellvsAllotherWithoutBMpreBdiffBD.minOverlap1.log2FC1FDR0005.upinSplenicBcell.center400bp.bed.bw -a 500000 -b 500000 -bs 20000 --referencePoint center --samplesLabel stable hep myo bcell -p 20 -R regions/Boundaries/GSE93431_UNTR.50kb.cool.HDF5_diamond-insulation.800kb.1000kb.txt_filter-0.1.bed -o Mouse.stable.specific.CBS.peakDensity_ON_800kbAround_GSE93431_UNTR.50kb.cool.HDF5_diamond-insulation.800kb.1000kb.txt_filter-0.1.matrix.gz

12.4 output:

  • data/data/countmat/StableSpecificCBS_peakdensity_on_diamondBoundaries/*matrix