Question: Caveats of Including Intronic Reads in Single Cell Sequencing data?
gravatar for ericvaughn11
2.0 years ago by
ericvaughn110 wrote:


I've just done some nuclear sequencing and found a high proportion of my sequencing output consisted of intronic reads (about 50%) compared to exonic reads (about 22%). Because the nucleus is likely a sample of mRNA produced in the last 30 minutes or so (if anyone knows how fast RNA is transported out of the nucleus I'd be happy to know), I figure this makes sense, since it's likely that many more pre-mRNA are captured in nuclear sequencing.

I'd like to include the intronic reads in the output to my gene-barcode matrix, though intuitively, it feels like there's some caveats to this. I'm not very familiar with sequencing, so if anyone could advise me on potential issues this might introduce, I'd be very happy to know.

Best, Eric

rna-seq • 496 views
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