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satijalab / seurat-wrappers

Community-provided extensions to Seurat
GNU General Public License v3.0
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Can I add spliced or unspliced info to my SeuratObject? #111

Closed AAA-3 closed 3 years ago

AAA-3 commented 3 years ago

Hello every one!

I have 10X Genomics output from multiple runs. From each run, I created a Seurat Object from the output/filtered_gene_bc_matrices/ folders and then merged them into 1 seurat object.

I used the above merged object for all my clustering analysis and have exported this all as an RDS file.

I want to know how I can include spliced and unspliced mRNA data into the Seurat object so that I can do some scVelo RNA velocity analysis. Any thoughts?

This vignette seems to run Seurat analysis from a loom file that already has splicing info - how do I go the other way around?

samuel-marsh commented 3 years ago

Hi @AAA-3,

You have to run Velocyto or another aligner that supports output of spliced and unspliced reads in order to do this (hence the vignette starting from a Velocyto output loom file). 10X cell ranger outputs are by default just the spliced counts (or a total or spliced and intron counts if option selected in CR5+).

Best, Sam

AAA-3 commented 3 years ago

Yeah I figured there would be no work around - I’m was hoping to keep my Seurat analysis because repeating it after velocyto would (maybe) change some of the output etc. since Velocyto has it’s own exclusions. Shouldn’t be too major - thanks!!