Hi-C ES and neocortex from Bonev et al. 2017 on mm39

Reanalysis of some Hi-C from Bonev et al. 2017 with HiCUP v0.9.2 This is a third-party reanalysis of some datasets of GSE96107 to provide a more friendly format. Hi-C ES from Bonev et al. (reanalysis of GSM2533818 to GSM2533821) Hi-C ncx NPC from Bonev et al. (reanalysis of GSM2533835 to GSM2533838) Hi-C ncx CN from Bonev et al. (reanalysis of GSM2533839 to GSM2533842) DATA PROCESSING DETAILS: Fastq were retreived from SRA with fasterq-dump version 3.0.3 They were processed with HiCUP v0.9.2 specifying DpnII, ^GATC as enzyme Pairs were extracted with custom version of hicup2juicer. The pairs of 4 replicates were concatenated. Pairs were split by chromosome and sorted with cooler csort version 0.9.1 Matrices were generated with cooler with bins of 5kb or 20kb and balanced with option –cis-only All scripts are available at https://github.com/lldelisle/Hi-C_reanalysis_Bonev_2017 genome build/assembly: mm39 processed data: *csort.gz: tabulated file in juicebox format ( with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.) processed data: *cool: cool file with balanced matrix at 5kb or 20kb