HiC-Correlation

Step 1: download straw

https://github.com/aidenlab/straw

Step 2: extract matrix from .hic files

Example

bash run4GenData.sh Rao

Step 3: modify .list files

List the matrix which extracted from straw (i.e .txt files) you want to compare into .list.

Example

***.list/
HiC-Pro data/Rao/Rao_hicpro_NONE_chr1_10kb.txt
HiCUP data/Rao/Rao_hicup_NONE_chr1_10kb.txt
Hi-CPIPE data/Rao/Rao_hicpipe_NONE_chr1_10kb.txt
Hickit data/Rao/Rao_hickit_NONE_chr1_10kb.txt
Bin3C_5 data/Rao/Rao_5_NONE_chr1_10kb.txt
Bin3C_5SP data/Rao/Rao_5SP_NONE_chr1_10kb.txt

Step 4: run correlation codes

Example

bash run4analysis.sh Rao

or

Rscript ./calCor-4-ncontacts.r list/Rao_NONE_chr1_10kb.list Rao_NONE_chr1_10kb

Please see illustration in run4GenData.sh and run4analysis.sh to modify the TODO parts for other analysis.