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wupengomics / scBS-map

Single-cell Bisulfite Sequencing Data Mapping
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Queston about PE/SE reads in end2end alignment #2

Open xiaonian92 opened 2 years ago

xiaonian92 commented 2 years ago

Hello there, thanks for the nice tool, I have some questions when using this and hope you can help me: 1) How to align PE data? I notice that in "ii align-end2end" you only use "-f Sample.R1.trim.fastq.gz" which is R1 in PE mode, what about R2? why do you use -1 R1.fq -2 R2.fq just as BS-seeker does? 2) Why do you prefer SE mode alignment for PE data? In my idea, reads after BS convertion are tended to have a higher error mapping rate, and PE mode alignment could help to revise to some extent. Is this right?

Thanks!

timpeters82 commented 4 months ago

Hi Peng,

Seconding a response to this question. I have PE reads for scBS-Seq, and from your code it is unclear how scBS-map ought to handle PE data.

Best, Tim