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theislab / cellrank

CellRank: dynamics from multi-view single-cell data
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Pipeline from Seurat object to CellRank #1204

Closed mainharryHR closed 2 weeks ago

mainharryHR commented 2 weeks ago

... Dear Team,

I am curious if there is a pipeline starting from Seurat object to CellRank to do the trajectory or velocity ?

I am working with 30 patient samples. it seems I need to start from the files before alignments one by one in order to get the unspliced RNA. The files are super big as well. Is there any way to get around that?

Any comments are welcome.

Best

Marius1311 commented 2 weeks ago

Hi @mainharryHR, if you want to estimate spliced and unspliced counts, please check our velocyto, kalisto, or related tools! Other questions related the RNA velocity estimation are probably best posted in the scVelo repo.

WeilerP commented 2 weeks ago

Thanks, @Marius1311. Closing the issue since it is not related to CellRank directly.

mainharryHR commented 2 weeks ago

Hi @mainharryHR, if you want to estimate spliced and unspliced counts, please check our velocyto, kalisto, or related tools! Other questions related the RNA velocity estimation are probably best posted in the scVelo repo.

Thank you very much for your suggestions. I am new in this field, Sorry for the dumb questions. I am working with Seurat object. I am wondering where to get the unspliced RNA information. I feel I need to use the CytoTrace for Seurat object. Any comments are welcome.

Thank you all.

WeilerP commented 2 weeks ago

You do not need unspliced counts for CytoTRACE. See here or here for an example workflow.