Closed Lucas446 closed 1 year ago
Hi, was the bed file sorted? It has to be sorted by chromosome. Otherwise regions are skipped. Best
Ralf
Hi,
It was just because of the --range option. Every pairs having contact outside of the range are not considered.
Thanks a lot !
Hi,
I give as input to hicAggregateContacts function a .bed file containing 388 regions.
When looking at the output file generated by "--outFileContactPairs" option I only find 26 regions being tested.
Do you know why 108 regions has been filtered out ? (I can see that some pairs have 0 contacts, so it is not filtering out the regio that doesn't interact)
Thanks for your help, Best, Tanguy