search

XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
Other
53 stars 16 forks source link

juicer v2 .hic file as the input? #51

Closed xunchen85 closed 1 year ago

xunchen85 commented 1 year ago

Hi Xiaotao,

How could I use neoloopfinder with the .hic file in V9 format generated by the latest juicer tool? Apparently hic2cool does not support the conversion of .hic V9 file to mcool/cool.

Thanks, Xun

XiaoTaoWang commented 1 year ago

Hi Xun, can you try my another software HiCLift (https://github.com/XiaoTaoWang/HiCLift)? While it was initially developed for coordinate conversion for chromatin contacts, it can also be used for format conversion by setting the "--in-assembly" and "--out-assembly" parameters to the same value.