Single Cell mRNA Seq basic question
If an average human somatic cell has approximately 12k transcripts of mRNA floating around, how do we (for example) get a mean reads per cell of 100k? Shouldn't you get 12k mean reads per cell
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there are lots of other non-mRNA transcript floating around in the cell (and yes despite poly-A capture you will pick some of them up as well)
EDIT: ok, my bad, indeed number of reads is something very different than number of transcripts as goodez said.
Number of reads you will get is very different than the number of transcripts due to shearing the DNA and PCR amplification.
So are two reads with the same UMI considered two reads or one read?
They are two reads but they originated from the same fragment.
I have seen estimates of 500k transcripts. It will vary by cell type, though. And, as others have pointed out, one transcript can produce multiple reads.