Question: RNAseq with quantseq
0
gravatar for kanwarjag
3.4 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

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.

rna-seq • 1.2k views
ADD COMMENTlink modified 3.4 years ago by WouterDeCoster44k • written 3.4 years ago by kanwarjag1.0k

Tagging michael.ante

ADD REPLYlink written 3.4 years ago by WouterDeCoster44k
0
gravatar for WouterDeCoster
3.4 years ago by
Belgium
WouterDeCoster44k wrote:

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).

ADD COMMENTlink written 3.4 years ago by WouterDeCoster44k

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?

ADD REPLYlink written 2.9 years ago by enxxx23230

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

Yes

ADD REPLYlink written 2.9 years ago by WouterDeCoster44k

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?

ADD REPLYlink written 2.9 years ago by enxxx23230

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

ADD REPLYlink written 2.9 years ago by WouterDeCoster44k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1043 users visited in the last hour