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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Question: Does zUMIs perform any frameshift correction for SPLiT-seq? #298

Closed jeremymsimon closed 2 years ago

jeremymsimon commented 2 years ago

I see you implemented a frameshift correction of barcode sequences for other single-cell platforms many releases ago, but I can't quite tell from your code if this applies to SPLiT-seq reads too. Can you comment on that?

cziegenhain commented 2 years ago

Hi,

From my understanding of the SPLiT-seq libraries there is no frameshifting expected, so I have not used the frameshift correction for this protocol before: https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup#combinatorial-indexing

As an example where I have used it: ddSeq/SureCell there is an intentional frameshift to make more base diversity while sequencing https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup#ddseq--surecell-3

Best, Christoph

jeremymsimon commented 2 years ago

Okay good to know. SPLiT-seq certainly doesn't have intentional frameshifts, but I think it can happen at some frequency due to sequencing error. No need to incorporate any fixes for this currently