How to obtain the counts matrix with ambient RNA removed?

[wangdlpbr]

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]

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]

Thank you and look forward to hearing from you

[wangdlpbr]

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

[wheaton5]

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]

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.