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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
658 stars 172 forks source link

Kallisto for Parsebio #427

Open rootze opened 9 months ago

rootze commented 9 months ago

Hello Kallisto developer,

Thank you for this excellent tool. I would like to know if Kallisto works on Parsebio split-pool snRNA-seq, which I have heard the rumor for quite a while. If you can kindly share any information and point me to figure out how to run it on Parsebio data, that would be great!

Thanks

Yenaled commented 9 months ago

See the end of this manual here (requires pip installing kb_python version 0.28.2):

https://www.biorxiv.org/content/biorxiv/early/2024/01/23/2023.11.21.568164/DC1/embed/media-1.pdf

Currently migrating this manual to a website, but yeah, kallisto is a great tool for split-seq: just one command can give you all the matrices you could ever need. The counts_unfiltered_modified/cells_x_genes.total.mtx output is probably the one that you’d to use for snRNA-seq (it agrees the most with what ParseBio’s software does: collapsing oligodT and randO priming into a the same barcode and summing up exons+introns+junction counts). Let me know if you have any questions!