simpleaf Processing SplitSeq / ParseBio data with simpleaf

Hi @rob-p and team

We have some ParseBio data that it would be nice to process with simpleaf.

I found this tutorial for alevin-fry: https://combine-lab.github.io/alevin-fry-tutorials/2022/split-seq/ It looks like the only difference to what simpleaf wraps around is using a --splitseqV1 flag in the salmon alevin call. However I searched the simpleaf documentation page for "splitseq" / "split seq", and that didn't turn up any results.

Does that mean that at the moment, simpleaf isn't set up for splitSeq / ParseBio fastq formats? If that's the case, please add a small +1 in favour of this task on your list of possible future tasks :)

Thanks! Will

Sep 18 '23 14:09 wmacnair

Thanks @wmacnair! I think this would be a prime candiate for either our upcoming seqproc feature (cc @noahcape & @Daniel-Liu-c0deb0t) or our the workflow + patch system. Right now, one could do this with simpleaf, but they would have to process the reads with splitp first (though it supports streaming transformation).

--Rob

Sep 18 '23 15:09 rob-p

Ah ok, so a very quick fix would be updating the splitseq tutorial to show how to do it with simpleaf?

Will

Sep 18 '23 16:09 wmacnair

Yes, I believe so. I'll chat with Dongze about this and ping you when we have something.

Best, Rob

Sep 19 '23 14:09 rob-p