Help interpreting contact map

[Levi Bauer]

Hello,

I'm currently working on two assemblies for plant species with very large genomes (~2 Gbp). Both species are within the same genus, diploid, and are expected to have 12 chromosomes based on previous studies. For both species, I have an 'extra' 13th scaffold that is an order of magnitude smaller than the other pseudomolecule scaffolds, and significantly larger than the debris scaffolds after it. It doesn't have strong hic contacts with any of the pseudomolecules outside of telomeric regions, where it has contact with every pseudomolecule's telomeric region. We originally assumed it was mostly repeat sequence, but after a busco analysis we realized it was rather rich in busco hits. The species with the better contact map has 22% of single copy, complete buscos aligning to the 13th scaffold, whereas the species with the poorer quality map has ~30% of single copy buscos. 

Have you seen/heard of anything like this before? We're currently at a loss for how to deal with it, and I'm hoping you have some insights. 

Below is a screenshot from the species with a stronger contact map, hopefully demonstrating what I'm talking about.

[Robert King]

Chloroplast? Blast it to ncbi to make sure not contamination?

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[Olga Dudchenko]

It's hard to judge from a static image. Seems to be too big for a chloroplast? If you send an interactive map or at least zoom in, it might be of help. Also I am guessing you are showing a balanced map which hides some potentially insightful info re coverage. Best, -Olga

[Levi Bauer]

I've tried to find information on how to send an interactive map (I didn't know that could be done). Is there documentation somewhere? I checked through the cookbook and couldn't seem to find any. 

[Ruqayya K]

Hi Levi, 

Interactive maps sessions can be visualized and shared in Juicebox.js, the web browser version of Juicebox. It can be accessed online here: https://aidenlab.org/juicebox/

Here is the corresponding Juicebox.js paper: https://www.cell.com/cell-systems/fulltext/S2405-4712(18)30001-2

This information is listed on the DNA Zoo Methods page above the Genome Assembly Cookbook. 

Thanks,

Ruqayya Khan