Processing single-cell RNAseq counts with simpleaf (alevin-fry)

Simpleaf is a faster and more efficient alternative to other counters, such as cellranger, and it works with other single-cell chemistries. It is a wrapper for Alevin-fry and is made by the same lab that created the Salmon RNAseq aligner.
Simpleaf is still in development as of making this video. Do not be surprised if the workflow changes slightly in the future.
Github notes:
github.com/mousepixels/sanbom...
references:
combine-lab.github.io/alevin-...
www.nature.com/articles/s4159...

[@avp300]

Thank you !

[@YC-ut1ff]

Thanks for the tutorial! Have you used this pipeline on 10x Fixed RNA profiling? It seems that velocyto doesn't support 10x Fixed RNA profiling. The count generated from velocyto is way lower than cell ranger.

[@JAIRAJMATHUR]

Thank you for the tutorial! Are you also planning on creating spaceranger and squidpy tutorials?

[@sanbomics]

Maybe eventually... not a lot of time recently to make videos. But hope to knock some out of my queue shortly

[@chrisjmolina]

Did using this pipeline alter your output data? You said you had less dropout, does this mean the downstream analysis yielded different clustering and/or gene expression patterns compared to Cell Ranger?

[@sanbomics]

I haven't compared downstream analysis. The differences will for sure be there, but they will probably be minimal. I doubt it will change your conclusions broadly.

[@lst595991]

It took me several days to install by conda before it was successful.😂

[@sanbomics]

Please let us know what error you were getting and how you fixed it in case anyone else comes across the same issue!