search

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
410 stars 181 forks source link

collisions.awk does not work for contig names #224

Closed qisun2 closed 2 years ago

qisun2 commented 3 years ago

The collisions.awk would not work if my reference genome have contig names not like "chr1" "chr2". For now I just modify the awk scripts by removing the name check.

Lattesnow commented 3 years ago

I have the same problem. You can try to use hg19 as the reference genome will solve this.

nchernia commented 3 years ago

This is not actually a problem we encounter so I'm not sure why you think they need to look like chr1, chr2 etc. For instance we use Juicer to assemble genomes de novo.

Please post the version of Juicer you're using and what the failure actually is.

On Fri, Jul 16, 2021 at 1:06 PM Lattesnow @.***> wrote:

I have the same problem. You can try to use hg19 as the reference genome will solve this.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/224#issuecomment-881592701, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW5XARQG43ZB563JQRDTYBRJXANCNFSM44PC64VQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

sa501428 commented 2 years ago

If there are still questions on this, please ask them on the forum: aidenlab.org/forum.html