Large difference in mean reads per cell from cellranger and nCount_RNA from Seurat, is it a problem?
I have single cell RNA-seq from PBMCs. Cellranger gives a mean reads per cell by dividing the total number of reads by the estimated number of cells. After loading into Seurat I can get the true mean reads per cell by taking the mean of nCount_RNA.
For the 5 samples I have, the mean reads from Cellranger are between 30k and 98k. The mean nCount_RNA is between 4100-4800.
Is this normal? Where are most of the sequencing reads going, is this from sequencing RNA from burst cells?
• 2,565 views
•
link
updated
by
swbarnes2
•
written
by
piloc16566 •
•
written
by
piloc16566 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
STARsolo ; Reads are NOT mapped to transcriptome
written by gdfsnkfns •
-
cell ranger count
written by archanaverma433 •
-
comparison between STARsolo and cellranger
written by dalibenam64 •
-
Does it make sense to analyze snRNA-seq data with low nUMI per gene?
written by fifty_fifty •
-
valid UMIs in STARsolo output?
written by hamarillo •
-
Issues with Quantification with STARsolo
written by sroth •
-
why starsolo estimated cell number very different from cellranger.v5
written by Anny •
-
What is the best practice for analysing single-cell data with low sequencing depth?
written by VolEr •
-
Estimated Number of Cells in 10X vs Cells in Seurat
written by Payal
-
How to find percentage of a gene (eg.Ppbp) for condition A and condition B from 10X Single Cell RNA…
written by bioinforesearchquestions
I never worked directly with CellRanger only with its final output. Usually what is imported to Seurat is the filtered result of the CellRanger pipeline. Are you sure that you're looking into the same files with CellRanger?
Did you check if the number of cells in each sample between Seurat and cellranger is the same?
Are you sure you aren't mixing up reads and UMIs? Seurat is importing from a file of UMI counts.