2D Functions

Convert mapped Hi-C reads to .hic file

A. Purpose
To create a binary hic format file containing contact matrices at different resolutions and normalized by different methods from a text file describing mapped Hi-C reads

B.Test Data
An example test data is the GM06990 cell line data, that can be downloaded from link below:\

1. GM06990 Cell line:

• Bowtie2: http://sysbio.rnet.missouri.edu/bdm_download/GenomeFlow/GM06990/GenomeFlow_formatted.bowtie2.input\
• Bwa: http://sysbio.rnet.missouri.edu/bdm_download/GenomeFlow/GM06990/GenomeFlow_formatted.bwa.input.\

C. Output
A binary .hic file containing contact matrices

D. Running
Access the function from the menu toolbar: 2D-Functions/Convert to HiC

E. Convert mapped Hi-C reads to .hic file GUI