Chapter 18 HiC Coolpup Loops APA

18.1 Description

compute the pileup matrix for mouse-WTDM mouse-Bcell loops, loops are grouped into St-St loops and Spe-Spe/Non loops based on CBS sets

18.2 Input data

• data/DiffBD/Mouse-SplenicBcellGSM3027985vsAllotherWithoutSplenicBcelGSM2652790diffBD.minOverlap1.log2FC1FDR01.D210325upinSplenicBcellGSM3027985.bed
• data/DiffBD/Mouse-MTvsAllotherdiffBD.minOverlap1.log2FC1FDR001.upinMT.center400bp.bed
• data/DiffBD/Mouse-multipleCells-stable-CBS.center400bp.bed

18.3 Processing

• pileup

coolpup.py --weight_name KR --n_proc 20 --ignore_diags 0 --mindist 0 ../../cools/WT_DM.allValidPairs.res5kb.cool ../../regions/Mouse-MultiCells-Loops/withoutchr/GSE98119_Vian-2018-activated_B_cells_24_hours_WT.hic_5k10kloops_SpeSpeANDSpeNON_CBS.bedpe

18.4 Output:

• data/Pup-npfiles/loops-classby-CBS