Chapter 14 HiC Loops Preprocess

14.1 description

call loops using HICCUPS, for myocyte using resolution of 3k, 5k and 10k, for B cell using 5k and 10k

14.2 input data

  • GSE98119_Vian-2018-activated_B_cells_24_hours_WT.hic.50kb.cool
  • GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT.hic
  • WT_DM.allValidPairs.hic

14.3 processing

time java -Xmx8g -jar /lustre1/lch3000_pkuhpc/liuyt/software/bin/juicer_tools_1.13.02.jar  hiccups -r 3000,5000,10000 -k KR -f 0.1,0.1,0.1 -p 6,4,2 -i 10,7,5 -t 0.02,1.5,1.75,2 -d 15000,20000,50000 --ignore_sparsity  /lustre1/lch3000_pkuhpc/liuyt/ChenQ/Hi-C/hicfiles/WT_DM.allValidPairs.hic WT_DM.allValidPairs.hic_3k5k10kb_loop

14.4 output:

  • data/HiC/loops