Question

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

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2.5 years ago

Claire • 0

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

cellsingleRNAseq RNASeq • 762 views

ADD COMMENT • link 2.5 years ago by Claire • 0

score 2 · Accepted Answer · 2022-06-13

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2.5 years ago

ATpoint 85k

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.

ADD COMMENT • link 2.5 years ago by ATpoint 85k

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

ADD REPLY • link 2.5 years ago by Claire • 0

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Run FastQC just on Read 2.

ADD REPLY • link 2.5 years ago by GenoMax 147k

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Thank you GenoMax

ADD REPLY • link 2.5 years ago by Claire • 0