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pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data
https://kallistobus.tools/
MIT License
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Nucleus workflow for RNA Velocity - no spliced/unspliced layers in file output #42

Closed AlinaKurjan closed 2 years ago

AlinaKurjan commented 2 years ago

Hi, thank you so much for developing this amazing tool! I've been wondering about the single-nucleus RNAseq workflow for RNA velocity. I've tried generating h5ad files following the kb RNA velocity tutorial using both --workflow nucleus and --workflow lamanno (didn't work) options. The nucleus workflow runs well, however the h5ad output file does not contain any layers, i.e. no spliced and unspliced reads stored within, while the loom output file fails to load in over 30 mins. I think this might be a bug but not sure.

Could you please let me know exactly what the workflow nucleus does since it is recommended for snRNAseq velocity. Does it take into account that there will be a high percentage of unspliced counts? Also, if you can, please let me know if there is a straightforward way of loading the spliced/unspliced matrices into the layers of h5ad output. I've tried a few suggestions with little success.

Thank you for your time!

AlinaKurjan commented 2 years ago

this question is answered in the kb_python github, issue 171: https://github.com/pachterlab/kb_python/issues/171