Query regarding generating input files

[Anubhooti -]

Hi,

I understand that the input 'interaction' file requires raw contacts, but I only have the probability contact matrix of a single chromosome, as I am looking for significant interactions in a single chromosome only. Is it possible to generate the input 'interaction' file from that matrix? What parameters will I have to change while generating both the input files for such a case and also while further running FitHiC2. The two issues: 1) having contact probability matrix instead of raw counts 2) use for a single chromosome only.

Thanks,

Anubhooti

[Ferhat Ay]

Hi, use for a single chromosome is not an issue at all. I do not know what you mean by contact probability. If you mean normalized contact counts divided by row sum then you can multiply back with the row sum (if you know that) and maybe round to the nearest integer. Honestly, I can't guarantee results will make sense unless you have the raw contact count matrix. Sorry

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