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XPRESSyourself / XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data
https://xpresspipe.readthedocs.io/en/latest/
GNU General Public License v3.0
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Allow riboseq to handle paired end reads of both input and RPF libraries #50

Closed jdreyf closed 3 years ago

jdreyf commented 3 years ago

@j-berg: It appears that paired end input libraries are accommodated with peRNAseq, but I don't see any mention of paired ends in the riboseq documentation at https://xpresspipe.readthedocs.io/en/latest/content/riboseq.html.

We have paired end input and RPF libraries, so we would like xpresspipe to handle this case.

Thanks for your continued help.

j-berg commented 3 years ago

Hi @jdreyf , sorry for the slow response. By default, we did not include PE capabilities with the riboseq module as more often then not, ribosome profiling is performed using SE sequencing due to the small size of the RPFs. If you have PE total RNA, I would process these samples separate from the RPF samples using the peRNAseq module, but I would have some hesitancy combining SE RPF and PE RNA reads in the same analysis, unless you were to include this distinction as a factor during differential expression analysis. I may be missing the point, but as far as I am aware, I have not seen any PE RPF library generation methods (or at least, none that are used widely).