FitHiC2 with replicates

[Daiane Hemerich]

Hi,
I have 2 *validPairs.txt.gz files, from 2 replicates on the same experiment.
How do I run the FitHiC2 pipeline described in PMID 31980751 with 2 replicates?
Thank you in advance,

[Ferhat Ay]

You can either combine (simple concatenation) the two validPairs files before creating contact maps and doing the normalization and run fithic on the combined, or use each one separately and then combine the fithic results after the fact. Depending on whether these are biological replicates or technical replicates one may make more sense than the other. 

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