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COMBINE-lab / simpleaf

A rust framework to make using alevin-fry even simpler
BSD 3-Clause "New" or "Revised" License
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Processing SplitSeq / ParseBio data with simpleaf #104

Open wmacnair opened 9 months ago

wmacnair commented 9 months ago

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

rob-p commented 9 months ago

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

wmacnair commented 9 months ago

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

Will

rob-p commented 9 months ago

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

Best, Rob