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Results tagged with scrnaseq
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user 64
Use this tag for questions related to single-cell RNA-seq.
3
votes
Accepted
Why do I have >10,000 cells in the 10X matrix produced by cellranger?
The raw data from cell ranger contains all of the barcodes detected in the experiment. These raw barcodes are filtered by cell ranger to identify the barcodes that likely represent cells rather than …
- 752
2
votes
scRNA-seq differential transcript usage
There is a paper that takes advantage of transcript compatibility counts (TCCs). A TCC describes all of the potential transcripts that a cDNA alignment can be derived from. The senior author, Lior Pa …
- 752
1
vote
Accepted
Processed spliced and unspliced count matrices for existing scRNA-seq atlases
I am not sure if there are preprocessed datasets available, however, Kallisto + Bustools was designed specifically for the rapid quantification of spliced and unspliced transcripts.
- 752
1
vote
Handling sample identity in aggregated 10x libraries?
You have to keep track of the file order you used for aggr. The suffix number represents which represents the aggregated sample. You could store this information in a text file and load it into R ind …
- 752
1
vote
Accepted
Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amoun...
I am inclined to agree with you that the reads-per-cell is dependent on the cell type and cell cycle state. In the datasets I have analyzed, I observed that immune cells tend to have far fewer reads …
- 752