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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicAggregateContacts: FileContactPairs uncomplete #826

Closed Lucas446 closed 1 year ago

Lucas446 commented 1 year ago

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

ralfgilsbach commented 1 year ago

Hi, was the bed file sorted? It has to be sorted by chromosome. Otherwise regions are skipped. Best

Ralf

Lucas446 commented 1 year ago

Hi,

It was just because of the --range option. Every pairs having contact outside of the range are not considered.

Thanks a lot !