Hi-C data

[ValWood]

We have a triage section for Hi_C data, but we can't host it yet.

This paper PMID:27548313 is a HI-C dataset, with some curation, so I don't want to classify as Hi-C
We can resolve this when we can triage as "curatable" and something else
In the meantime, we need a list. This is probably not the best place but I'll sort that once I have some time.

We have tickets related to this on various trackers

[ValWood]

This is a placeholder ticket, nothing to do yet

[ValWood]

@Antonialock "3C" type of analysis, showing physical clustering of meiotic DSB hotspots by ligation, immunoprecipitation, and deep sequencing
Fowler et al., PNAS 2018 (Figure 4B and C, and S7A and B)
(this should probably move to a page where we collect 3C data).
PMID: 30217891
(https://github.com/pombase/website/files/3371680/Fowler.et.al.PNAS.2018.complete.pdf)

[kimrutherford]

We have a triage section for Hi_C data, but we can't host it yet.

JBrowse v2 supports Hi-C tracks: https://jbrowse.org/jb2/docs/user_guides/hic_track/

V2 issue:

• Investigate JBrowse v2 #2038

[ValWood]

This might be a nice new. feature for the next paper...

@PCarme do you think this would be useful? I'm not sure how many HI-C datasets we have for fission yeast

[PCarme]

Yes, this could be useful. I don't know how many Hi-C papers there are in S. pombe, but I could look into it

[ValWood]

I just remembered!

https://curation.pombase.org/pombe/view/list/triage_3d_genome_organization?model=track

[kimrutherford]

JBrowse v2 supports Hi-C tracks: https://jbrowse.org/jb2/docs/user_guides/hic_track/

The data needs to be in .hic format for JBrowse:
https://github.com/aidenlab/juicer/wiki/Data#hic-files

I had a look at PMID:27548313. It says:

Data described in this paper were deposited into the National Center for Biotechnology Information
Sequence Read Archive database with accession number SRP061635.

So they're submitted the reads but there is no mention of depositing the processed data anywhere.

This software can process reads into .hic files: https://github.com/aidenlab/juicer
but I don't think we necessarily want to be doing that ourselves.

[ValWood]

OK @PCarme could you check the HI-C data for .hic files.
If there is none, we can mail the authors for the processed files.
I'm sure they will comply if we say they will be announced as the firsr Hi-C tracks in JBrowse.

[ValWood]

Actually I will put out a call and we'll see who responds.