Do we trim only second read in single cell RNASeq or both?

Question

[Claire]

Hi everyone

Do we trim adapters only in second read r_2 in single cell RNASeq or both? Or we should not trim at all? Thanks

Answer 1

[ATpoint]

Run fastqc, then you know. If you are talking about 10X then, if there are adapters, you probably only need R2 so the cDNA read, even though the aligner might probably just softclip it off. I personally feel safer to trim in case of notable adapter presence, which if library prep went well should not or rarely be the case.

[Claire]

Yes, talking about 10X. Thanks so much ATpoint.

[GenoMax]

Run FastQC just on Read 2.

[Claire]

Thank you GenoMax