I ran a question two days ago, trying to work out why some RNAseq data that I was analysing for colleagues wasn't particularly fruitful in differentiate genes (RNAseq comparisons (tophat->HTSeq->edgeR) return only a few sig diffs, and all snRNA. Pos. bias? Further options?) and we came to the conclusion that "it is what it is".
However, I hadn't thought to consider read depth originally, as I assumed (perhaps naively) that this would have been sufficiently decided before sequencing (and before I was consulted). I now see what I would consider a low-level of coverage, and I wonder if this could be affecting the results, particularly why we're observing these snRNA targets commonly (~12 out of 14 sig. diff genes).
This is a 2.5GB bovine genome with around 40million 2x75bp nextseq reads per sample.
Thanks for looking.