how to transform a sparse matrix to .hic file

Shawn Bai

unread,

Nov 29, 2022, 10:07:11 PM11/29/22

to 3D Genomics

Hi, all,

Now I downloaded a sparse matrix file(three columns: start of bin1, start of bin2, interaction counts). I want to visualize this in juicerbox, how can I transorm it into .hic file(even at single resolution).

Thanks,

Jiangshan

Moshe Olshansky

unread,

Nov 30, 2022, 5:59:12 PM11/30/22

to 3D Genomics

Hi Jiangshan.

You first need to convert it into the short format, which has 5 fields: chr1 start1 chr2 start2 counts

Then using the latest version of juicer (version 2.20) you can make a hic file out of it (with pre).

Regards,

Moshe.

David Katz

unread,

Apr 15, 2023, 8:53:37 PM4/15/23

to 3D Genomics

Can you please link to where the short form with five fields is specified?

Moshe Olshansky

unread,

Apr 17, 2023, 1:08:42 AM4/17/23

to 3d-ge...@googlegroups.com

Please look below:

https://github.com/aidenlab/juicer/wiki/Pre

--
You received this message because you are subscribed to a topic in the Google Groups "3D Genomics" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/3d-genomics/COQrPJtZXk8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/9cc93de1-0cc0-4a76-ba36-a0d4f8ee66b5n%40googlegroups.com.

Reply all

Reply to author

Forward