Running HiNT, hic_breakfinder, EagleC, and HiCTrans

DE Dan Daniel Erdmann-Pham
SB Sanjit Singh Batra
TT Timothy K. Turkalo
JD James Durbin
MB Marco Blanchette
IY Iwei Yeh
HS Hunter Shain
BB Boris C. Bastian
YS Yun S. Song
DR Daniel S. Rokhsar
DH Dirk Hockemeyer
request Request a Protocol
ask Ask a question
Favorite

HiNT36 was run with version: 2.2.7. hic_breakfinder38 was built from the master branch source downloaded from github, https://github.com/dixonlab/hic_breakfinder, using commit 30a0dcc6d01859797d7c263df7335fd2f52df7b8 (last updated in 2018). For hic_breakfinder the inter and intra chromosomal break files were provided by the Dixon lab as detailed on the github site. NextFlow pipelines to run both HiNT and hic_breakfinder can be found on the HiDENSEC github. EagleC37 was downloaded from https://github.com/XiaoTaoWang/EagleC and run with --prob-cutoff set to 0 so as to allow for calling of all possible variants. We were unable to install HiCTrans62 despite interactions with the authors due to deprecated dependencies of the hashmap R package.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A