Run the commands below, you will directory "ref/".
wget http://hiview.case.edu/ssz20/tmp.HiCorr.ref/HiCorr.tar.gz # download reference files
tar -xvf HiCorr.tar.gz
ls
ls ref/
There are 4 subdirectories under "ref/": "DPNII" "eHiC" "eHiC-QC" "HindIII"
The files in "eHiC" and "eHiC-QC" are for eHiC data generated in PMID: 32592681.
The files in "HindIII" and "DPNII" are for conventional Hi-C and in-situ HiC data.
Each directory mainly includes the follwing files, for example, in "DPNII"
ls ref/DPNII/
hg19.DPNII.frag.bed: fragment bed file for DpNII enzyme cutting site.
| chr | beg | end | fragment id | fragment size |
hg19.DPNII.blacklist includes the fragment overlapping the blacklist regions.
To run HiCorr with 5kb resolution, we need combine the neighbor fragments to achieve 5kb anchor size by using the hg19_DPNII_frag_2_anchor files
| fragment | 5kb_anchor |
After converting fragment to 5kb anchor, you will get anchor based files:
hg19_DPNII_anchors_avg.bed:
| chr | beg | end | anchor id | anchor size | averaged fragment size |
hg19_5kb_anchors_blacklist:
hg19.dist.401.group contains the 400 distance groups for 0-2Mb
| dist group id | group_start | group_end |
hg19_anchor_length.groups contains anchor length group
| length group id | group_start | group_end |
hg19.full.matrix contains all possible anchor pairs within 2Mb.
| anchor id 1 | anchor id 2 | zero | anchor loop size |
hg19.full.dist.len.stat
| anchor1 length group id | anchor2 length group id | dist group id | number of anchor pairs within 2Mb |
hg19.trans.possible.pairs contains number possible pairs counts from trans-interactions
| anchor1 length group id | anchor2 length group id | number of anchor pairs within 2Mb |
