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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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How to generate Bed containing the locus pairs (binned) and the contact count #412

Closed robeach78 closed 3 years ago

robeach78 commented 3 years ago

Hi I got to the point of running FitHiChIP, but I don't see a way of finding this file to input in the FitHiChIP:

Bed containing the locus pairs (binned) and the contact count:

Pre-computed locus pair file

of the format:

chr1 start1 end1 chr2 start2 end2 contactcounts

Bed=

Where do I get this file from HiC-Pro?

Thanks a lot, Roberto

nservant commented 3 years ago

Dear Roberto. Not sure whether FitHiChIP starts from the list of valid pairs (allValidPairs file extension). Or from a contact maps with the bins (bed format) and the counts (.matrix) files. N