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Hoohm / CITE-seq-Count

A tool that allows to get UMI counts from a single cell protein assay
https://hoohm.github.io/CITE-seq-Count/
MIT License
79 stars 44 forks source link

Filtering UMIs on read number #151

Closed rule-110 closed 2 months ago

rule-110 commented 3 years ago

I have a very deeply sequenced barcodes library and I expect a substantial amount of UMIs to not be real. We expect those "fake" UMIs to have very low read numbers. Is there a possibility to select only the UMIs that passes a certain read threshold. Also is it possible to have the distribution, like an histogram, of the number of reads per UMIs?

Thanks a lot

Hoohm commented 3 years ago

Hello @rule-110 ,

there is no thresholding at the moment. Mainly because I would rather have raw results come out for users to make their own choice post processing.

I would suggest a downsampling approach to get rid of the lowlevel UMIs for the moment.