Juicer pipeline to try other loop calling programs

[Yonatan Amzaleg]

Hello,

I've recently used Juicer to align my HiChIP files and make .hic files to view the interactions and to call significant looping via HICCUPS. The problem is the hpc from my university is a little tricky and I wasn't able to use GPU version of HiCCUPS and had to settle for the CPU version. I wanted to now try different loop calling programs to then compare it to the data I got from HICCUPS but most of the other programs require different types of input files (not .hic) for instance .bedpe, etc. I know I can't convert a .hic file to a .bedpe file, but I noticed that one of the outputs from user juicer.sh are .sam files which I think are the aligned files. My question is can I use those sam files to make the .bedpe files (i.e. is the alignment on those files also include the restriction enzyme I used and has been deduplicated, etc.)?

Thank you so much for such a wonderful tool!

Yonatan

[Neva Durand]

Thanks for your kind words!

For any kind of dense file, calling loops via input bedpe is going to be pretty space intensive. But you can try by converting the merged_nodups into bedpe. It should be fairly straightforward.

The format is here: 

https://github.com/aidenlab/juicer/wiki/Pre#long-format

I assume for the bedpe files, you would take input fields 2 and 6 (for chromosome) and convert to output fields 1 and 4; and then output fields 2/3 would be the position (field 3) plus whatever resolution (you could do just +1, or + read length), and output fields 5/6 would be the same but from the second position (field 7). Strand1 and strand2 (output fields 9/10) are given by input fields 1 and 5.

Another possibility is to take binned data from hic via Juicer Tools Dump or Straw and convert that to your bedpe, in which case you would use the beginning and end of bin number * resolution and the count would be the score.

Hope that helps! 

Best

Neva

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[Yonatan Amzaleg]

Thank you, I ended up using straw and this worked great!

I'm also interested in utilizing an aligned bam file from the juicer run and was wondering if the sam files are already de-duplicated and also are aligned with the restriction site I used (provided I provided the restriction enzyme cut sites for the genome when running juicer)? 

Thank you,

Yonatan

[Neva Durand]

For a dedupped bam file, it's best to use Juicer2, which can be found on the ENCODE branch of the Juicer github.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/edc6d846-f8ef-46a9-96b5-04b5c4535ec1n%40googlegroups.com.