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I follow this tutorial to generate loom file with spliced and unsplied counts, followed by converting loom to Seurat object.
Here are my scripts: ldat <- ReadVelocity(file = "path/to/loom/file")
bm <- as.Seurat(x = ldat)
saveRDS(bm, file = "path/to/rds/file")
object <- readRDS(file= "path/to/rds/file")
object[['RNA']] <- object[['unspliced']]
My questions are 1) Is it normal that the spliced/unspliced counts are much lower than the numbers I usually got from standard Seurat pipeline(without spliced/unspliced assay)? 2) Is there a way to filter out low quality cells (e.g. low nCounts_RNA, low_nFeature_RNA, high percent.mt) before I run SCTransform?
Thank you!
The text was updated successfully, but these errors were encountered:
Hi,
I follow this tutorial to generate loom file with spliced and unsplied counts, followed by converting loom to Seurat object.
Here are my scripts:
ldat <- ReadVelocity(file = "path/to/loom/file")
bm <- as.Seurat(x = ldat)
saveRDS(bm, file = "path/to/rds/file")
object <- readRDS(file= "path/to/rds/file")
object[['RNA']] <- object[['unspliced']]
My questions are 1) Is it normal that the spliced/unspliced counts are much lower than the numbers I usually got from standard Seurat pipeline(without spliced/unspliced assay)? 2) Is there a way to filter out low quality cells (e.g. low nCounts_RNA, low_nFeature_RNA, high percent.mt) before I run SCTransform?
Thank you!
The text was updated successfully, but these errors were encountered: