Kallisto for Parsebio

[rootze]

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]

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!