Ambient RNA Filtering with scAR prior to scVI

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I’m working with libraries prepped via 10x and our samples are from two different tissue types. I’ve been asked to preemptively adjust for ambient RNA given that these two tissue types are quite different and ambient RNA contamination could skew our data.

I am using scVI for my differential expression analysis. Would it be advisable to use ambient RNA adjustment packages like scAR or Cellbender prior to scVI? Or would scVI be sufficient enough to correct for ambient RNA on its own?

Thank you in advance. I’m still in the early phases of my bioinformatics training.
Rene

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You can run scVI after cell bender. Note that I believe the newest version of cellbender removes counts from the real observed count values, as opposed to imputing an ambient-free count. With these changes, so I would check to make sure you’re using the latest cell bender.

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