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ma-compbio / scGHOST

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
MIT License
18 stars 2 forks source link

Compatible with Fast-Higashi? #4

Closed AudreyBaguette closed 3 months ago

AudreyBaguette commented 3 months ago

I have single cell Hi-C samples with strong signal from structural variants that I wanted to mask, so I used Fast-Higashi instead of Higashi for them, removing regions with SVs. Can I still use scGHOST on my samples? The output format of the imputation is the same, so that's fine, but will it be a problem that I excluded some genomic regions? Thanks!

kairukuma commented 3 months ago

Hi Audrey, we've used Fast-Higashi outputs with scGHOST in the past. It should run, but the results may not be the same as if you run scGHOST with Higashi outputs. Can you elaborate on what genomic regions you've excluded?

AudreyBaguette commented 3 months ago

What do you mean by "the results may not be the same"? Does Higashi lead to better performance, or is it "only" a matter of different results without one being better than the other? I have a small list of breakpoints called by EagleC and I made a custom blacklist that is the ENCODE blacklist + custom list of regions of 2Mb around the breakpoints. They are all over the genome.

kairukuma commented 3 months ago

Fast-Higashi's outputs are different from Higashi's outputs, so you will probably get different subcompartment outputs. I can't say which result is necessarily better - it's up to you to decide based on your data.

For a small blacklist, I'm assuming the corresponding rows/columns in the scHi-C are zero'd out. In that case, they will be ignored by scGHOST and shouldn't impact the result.

AudreyBaguette commented 3 months ago

Awesome! Thank you very much! Just to make sure: the blacklist option is only available in Fast-Higashi, right? Not Higashi? (I am sorry if this is not the place to ask, but since it's all from your group, I hope it's ok)

ruochiz commented 3 months ago

Natively, yes, only Fast-Higashi implements the function to take a blacklist.bed file. But technically you can pre-filtered your contact pairs files to remove any contacts that overlap with regions in your blacklist

AudreyBaguette commented 3 months ago

Great! Thank you!