I am trying to use the FitHIChIP tool via HIChIP and HiC-Pro pipeline.
However, in FitHIChIP I need to input a bed file with columns:
chr1 start end chr2 star end contact_count
How do you generate this from any of the other two tools.
In HIChIP I have the mapped pairs but don’t see the counts of the score.
In the HiC-Pro I have the valid aligned pairs but again I don’t see the contact counts.
Help please thank you,