Batch effect issue in RNA velocity analysis
0
0
Entering edit mode
15 days ago
sarahmanderni ▴ 100

Hi,

Using Seurat to perform scRNAseq analysis for multiple samples (SCT + CCA integration and downstream analysis), what would be the recommended input assay to run RNA velocity using cellrank or scvelo? I am thinking to extract RNA assay, UMAP embeddings and clusters information to provide to scvelo but the RNA assay is not batch corrected. On the other hand not sure if using "integrated" assay as input for scvelo is a reasonable choice either.

RNA-velocity integration • 165 views
ADD COMMENT
1
Entering edit mode

I am not aware of any method for batch-aware velocity. There are GitHub issues at the scvelo repository and then have all (by best knowledge) no satisfying answer. I would run it separately per sample and then project the latent time onto the integrated dataset, knowing that you can only meaningfully compare the latent time within sample, not across samples. I would anyway not overinterpret velocity, it is after all a quite abstract metric, at least to me, that can be used for hypothesis generation, but nothing more.

ADD REPLY

Login before adding your answer.

Traffic: 2979 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6