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Published 20 hours ago • verified publisher icon satijalab

how to calculate spliced and unspliced counts in seurat object

Open skim245 opened this issue 4 years ago • 2 comments

I'm new to RNA velocyto and have a question on Velocyto

do we always have to go back to original raw file to estimate/calculate spliced and unspliced reads? or are there anyways that we can calculate them on subsetted seurat objects?

skim245 avatar May 11 '20 21:05 skim245

Hi @skim245 , as far as I know, you have to build the raw loom file from your bam file first, in order to be able to retrieve the spliced and unspliced reads.

MelissaSaichi avatar Mar 30 '21 12:03 MelissaSaichi

Hi @skim245 , as far as I know, you have to build the raw loom file from your bam file first, in order to be able to retrieve the spliced and unspliced reads.

Does this mean we have to create the loom file for the RNA velocity analysis and then re-run seurat analysis separately?

AAA-3 avatar Jul 19 '21 17:07 AAA-3