search

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Other
386 stars 182 forks source link

what is the Dumped_Pairs files about #648

Open Hanjiangna opened 2 months ago

Hanjiangna commented 2 months ago

Hi, I use HiC-Pro-3.1.0 to process my Hi-C data to mount haplotype genome chromosomes , and I've noticed a high proportion of Dumped_pairs (approximately 95% of the total reads). I am confused as to why my HiC-Pro results do not include Valid_interaction_pairs. Could you help me understand this? Valid_interaction_pairs 0 Valid_interaction_pairs_FF 0 Valid_interaction_pairs_RR 0 Valid_interaction_pairs_RF 0 Valid_interaction_pairs_FR 0 Dangling_end_pairs 0 Religation_pairs 0 Self_Cycle_pairs 0 Single-end_pairs 0 Filtered_pairs 1075688 Dumped_pairs 19635023

nservant commented 2 months ago

dumped_pairsare all pairs which are filtered out by the different parameters like inserts size, restriction fragments size or for which we were not able to reconstruct the ligation product

Hanjiangna commented 2 months ago

Hello "How can I adjust the parameters to reduce the number of dumped_pairs?" Thanks

nservant commented 2 months ago

remove the filters about insert size and restriction fragments size in the config file

Hanjiangna commented 2 months ago

LIGATION_SITE = AGCT MIN_FRAG_SIZE = MAX_FRAG_SIZE = MIN_INSERT_SIZE = MAX_INSERT_SIZE =

Without setting the above parameters, the result is as follows. Could you offer good suggestions regarding this ？ image Thanks