RNAseq with quantseq

Question

[kanwarjag]

Is there a particular advantage of using quant seq for RNAseq. I could not find any specific advantage except that it is 3' based sequencing. Any help ot pointing to the information will be helpful.

[WouterDeCoster]

Tagging michael.ante

Answer 1

[WouterDeCoster]

A few advantages would be:
-only 3' sequencing so therefore far less sequencing for the same expression quantification. As such the cost of sequencing is reduced, or you can multiplex more samples on the machine.
-less problematic for heavily degraded RNA

Obviously, you won't have alternative splicing/isoform usage, so it depends on what the aim of your research is. If you only care about expression levels, QuantSeq is fine (and definitely better than microarray).

[enxxx23]

Does R packages like edgeR, limma, DESeq2 work with QuantSeq 3' RNAseq? I mean, has anybody used and published results based on QuantSeq data analyzed with edgeR, limma, DESeq2?

[WouterDeCoster]

Does R packages like edgeR, limma, DESeq2 work with QuantSeq 3' RNAseq?

Yes

[enxxx23]

I meant that is there any reference (e.g. scientific article and not markerting material) which supports this? Do the authors of edger, limma, or DESeq2 concur with this?

[WouterDeCoster]

That question would probably be more appropriate for the Bioconductor support forum.