Optimal Preprocessing

[m-sterr]

Hi,

I have question regarding the optimal way for preprocessing counts for solo. In particular, should the input be raw counts or do you recommend some preporcessing? What preprocessing steps would that be?

Thanks a lot for your help!

[njbernstein]

The scVI model underneath solo requires the raw counts so no preprocessing should be done on the count level. It would be fine to remove cells with few. UMIs and cells with now UMIs should definitely be removed

[m-sterr]

Thanks a lot for your fast reply!