FitHiChIP issue input file

Hi, 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, Roberto

next-gen hichip

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updated 5.4 years ago by GenoMax

• written 5.4 years ago by roberto.ferrari1 •

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