My research group is trying to implement a pipeline for PARIS cited here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821472/ https://www.cell.com/fulltext/S0092867416304226
I have been trying to reproduce the code for HEK293T cells (one of the replicates) however I have been getting some trouble. I have emailed the group members but haven't received many replies.
I find myself getting a very high number of duplex groups (98,269 for HEK293T replicate 1 and 112,265 for HEK293T replicate 2) after filtering out stuff that overlaps with splice junctions and/or is not part of chr. This is not even close to the duplex groups obtained in the paper. This is no way close to the 56156 and 84742 found in the paper.
Some of these groups also may not be genuine interaction pairs.
Has anyone tried to implement this bioinformatics pipeline? I will appreciate any help that I can get.
