How to remove duplicated pairs in the validPairs？

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

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How to remove duplicated pairs in the validPairs？ #448

Closed biozzq closed 3 years ago

biozzq commented 3 years ago

Dear @all，

After performing -s mapping -s proc_hic -s quality_checks analysis in Hic-Pro, I only got the validPairs file but not allvalidPairs (options of Hi-C processing are as follows). In my study, one sample has one paired end reads, and I only focused on the end-to-end alignment. How can I generate the allvalidPairs file? Thank you.

MIN_CIS_DIST =
GET_ALL_INTERACTION_CLASSES = 1
GET_PROCESS_SAM = 0
RM_SINGLETON = 1
RM_MULTI = 1
RM_DUP = 1

Sincerely, Zheng zhuqing

biozzq commented 3 years ago

I know what I did wrong, I need to add the option -s merge_persample when running Hic-Pro.

Thank you for your nice tools.

Best regards,