Looking for appropriate software QC for bulk RNA seq.
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3.6 years ago
TonyCN ▴ 60

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:
1) Salmon
2) tximport
3) DESeq2,

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.

RNA-Seq QC R • 1.1k views
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I'd suggest taking a look at MultiQC and RSeQC. This article from omictools might also provide some suggestions.

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Is there anything for R? I know Fortran, Assembly, C/C++ and R. MultiQC and RSeQC look to be in python.

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You don't need to know the language to execute the tools.

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Ah, thank you. So they aren't APIs. Very sorry, I am just really rushed at the moment. I'll give them a proper look now then.

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