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Tryout Alevin for single-cell counting #9

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roryk opened this issue Jul 27, 2018 · 2 comments
Open

Tryout Alevin for single-cell counting #9

roryk opened this issue Jul 27, 2018 · 2 comments
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feature request request feature for any internal tool we use subcategory-scrnaseq single cell RNAseq pipeline

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@roryk
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roryk commented Jul 27, 2018

Alevin is a new mode in Salmon that handles single-cell (https://github.com/COMBINE-lab/salmon) (https://github.com/COMBINE-lab/salmon/blob/1695160fe8b7585b49fd7e2a458a7f867b311ebb/doc/source/alevin.rst). It only works for dropseq and 10x, but we could talk to Rob and company about how to add support for other schemes.
@roryk roryk added feature request request feature for any internal tool we use subcategory-scrnaseq single cell RNAseq pipeline labels Jul 27, 2018
@mjsteinbaugh
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@roryk I'm up for helping test this

@roryk
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roryk commented Aug 16, 2018

Awesome, someone opened up an issue on Mike's tximport repo asking about importing Alevin counts, so some other folks are starting to use it.

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@roryk @mjsteinbaugh