I would appreciate some assistance on a matter concerning QC of bulk RNA seq. I have a list of QC steps I ought to investigate before trying to pull out DEGs. I am in a position where I need results by yesterday; then I move onto theoretical chemistry, then pharmacology, you get the idea. Therefore, despite trying to cram in as much knowledge as possible, I really would appreciate any answers you can give.
I am taking the route:
with 2) and 3) in R - relatively straightforward. I would like to know whether there is an intermediary R package I can use that will perform a host of QC tasks over the read counts, mitigating all the code I would have otherwise had to write from scratch. A colleague has said scater, however, from what I understand, scater is for SC RNA seq and it feels counter-intuitive and a little bet untrustworthy (simply from intuition) to use on bulk.
Perhaps to judge what package would be most useful, my bulk RNA seq experiment is:
Sample Duration Treatment 1 Short Control 2 Short Drugged 3 Long Control 4 Long Drugged
Any recommendation on QC bulk RNA seq in R, would be massively appreciated. Thanks.