hicAggregateContacts use with different HiC matrix format

Question

[gregoire.stik]

Hi, I was wondering if it is possible to use hicAggregateContacts with HiC matrices from an external program. I have my in-house normalized matrices and I would like to know if there is a way to use hicAggregateContacts tools. Many thanks

Answer 1

[vivekbhr]

Hi. It depends on the format of your matrices. We provide a tool to convert between various HiC formats and HiCExplorer format. If you have your matrices in .cool format, or a homer-like format (all-to-all matrix), this would work.