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wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
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How to obtain the counts matrix with ambient RNA removed? #233

Open wangdlpbr opened 5 months ago

wangdlpbr commented 5 months ago

Hi,

Thank you for this great tool. My data has high ambient RNA, and I want to get the counts matrix with ambient RNA removed. I wonder if or how souporcell can do this?

Thanks!

wheaton5 commented 5 months ago

This isnt currently available. But it should be pretty easy. Right now im pretty busy. It would be easier to make a thing separate from the pipeline. I could prob do that in a few hours

wangdlpbr commented 5 months ago

Thank you and look forward to hearing from you

wangdlpbr commented 5 months ago

Do you have time to reply to my previous question recently?I want to get the counts matrix with ambient RNA removed. Thanks!

wheaton5 commented 5 months ago

Sorry. I have been busy. Happy to take pull requests if ud like to contribute. The ambient rna is assumed to be the average expression of the whole dataset. So if 1% of the dataset was from gene1 and ambient rna is 2% then for cell 1 gene1 was 5% of its data subtract off .02%. Avoid creating negative numbers. Thats how id approach it, but i havent done data analysis to see if this cleans things up or not.

wangdlpbr commented 5 months ago

Thank you for your reply.I recently successfully installed the package and am trying to follow the standard process. I am a novice and do not have much experience. Could you please show me how to modify the original analysis process in detail when you are free.