Hi-C data preprocessing

This repository introduces the step-by-step analytical pipleine for Hi-C data from raw fastq files to HiCorr bias correction and DeepLoop noise-reduction or signal-enhance contacts at 5kb-10kb resolution.

Please install HiCorr and DeepLoop in advance.

The example documents include mapping step, bowtie or bowtie2 index for hg19/mm10 are needed.

In the documents folder, you will find examples for processing:

Hi-C (restriction enzyme HindIII) in human Adrenal tissue

GSM2322539

in-situ Hi-C (restriction enzyme Mbol) in human GM12878 cell line, allele-resolved

GSE63525 (PMID: 25497547)

sn-m3C-seq(restriction enzyme DpNII) processed contact pairs in human Astro cell type

GSE130711 (PMID: 31501549)

Take HiCPro "allValidPairs" to run HiCorr and DeepLoop