The zip file contains the following files to perform TAD loop analysis. run_TADloop.sh: bash script to perform TAD loop analysis TADloop_cm_10k_top5.tsv: output of HiCMapTools plot_TADLoop.R:
The zip file contains the following files to perform TAD intra-density analysis. run_TADintra.sh: bash script to perform TAD loop analysis TADintra_cm_10k_top5.tsv: output of HiCMapTools plot
Merging four embryo HiC sets result in 2,035,932,051 S0 reads ( GSE 34453: Cell, GSE 61471: wild type, GSE 94115: female ,GSE 99105: male). fly.bimap is transferred from mergeEmbryo_cm_1000.n_contact
fly epiTADs is generated by hicpipe* based on top5 scaling factor with 10k window (10k_top5). It is formed in bed format where number represent epiTAD class:1:red:active 2:gray:null 3:PcG:blue<b
