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campbio / decontX

Methods for decontamination of single cell data
MIT License
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RNA velocity #18

Closed Sirin24 closed 2 months ago

Sirin24 commented 3 months ago

I have very basic questions.

I already generated loom files using velocyto from cellranger filtered matrix and bam files. Now if I am interested in running decontX, do I use the filtered matrix as input for decontX or the raw matrix? do I need to rerun velocyto after obtaining the corrected matrix from decontX?

joshua-d-campbell commented 2 months ago

Hi @Sirin24, Generally, yes, you can run decontX on the filtered matrix from CellRanger or any other tool. You can optionally supply the raw matrix to the background parameter which can sometimes help with decontamination when sorting or selection was done.

We haven't tested decontX in combination with velocyto so I can't give a you a definitive answer. The only thing decontX can do is remove a proportion of counts in each gene for each cell that is likely contamination from other cell types. It does not distinguish between intronic/exonic counts. It may be worth trying but hopefully using decontX won't change the velocities too much.