loom file for rna velocity

Question

[Chironex]

hi all, i'm trying to do a rna velocity analysis on a seurat object. I saw that loom files with spliced ​​and unspliced ​​transcripts are required, but, assuming that I only have the seurat object as input, how do I produce the loom files?

Answer 1

[Nitin Narwade]

You need to run RNA velocity CLI seperatly for your samples.

Link for the Tutorial

Then you can convert Seurat R object to loom file using SeuratDisk

OR

You can open velocyto loom files in R and do the downstream.

[Chironex]

Hi, I don't have the bam files. The Lab I'm working for just gave me the SeuratObject. So, if I understood, I cannot do the analysis with only the object, I need the bam files of my samples to generate loom files, is it correct?

[Nitin Narwade]

For velocity estimation, you need spliced and unspliced count and yes in this case you need bam files.

Regards, Nitin N.

[Chironex]

Thank you!