Question: DESeq2 for QuantSeq data
0
gravatar for andrebolerbarros
6 months ago by
andrebolerbarros10 wrote:

Hi everyone,

I've received data from RNA-Seq from my facility, which was sequenced using QuantSeq Kit. In theory, this kit allows for differential expression analysis cost-efficiently and with lower sequencing depth (less than 10M per sample, in comparison with some samples I got before, which had 30-35M per sample). The paper is here: https://www.nature.com/articles/nmeth.f.376.pdf

I know that, in addition to sequencing depth, we should also be looking into the experimental design in order to increase my statistical power. However, I found some one workflow designed for QuantSeq data especifically.

My question is if any of you have experience with QuantSeq data and know if it's possible to use DESeq2 directly in the data produced?

Thanks in advance!

deseq2 • 185 views
ADD COMMENTlink modified 6 months ago by cats_dogs20 • written 6 months ago by andrebolerbarros10
Answer: DESeq2 for QuantSeq data
1
gravatar for cats_dogs
6 months ago by
cats_dogs20
cats_dogs20 wrote:

There's nothing about this particular bioinfo workflow that is QuantSeq specific (though Hisat2 is now generally recommended over Tophat2). Yes, you can use DESeq2 on QuantSeq data.

ADD COMMENTlink written 6 months ago by cats_dogs20

Thanks for your response!

I asked that because I was searching for QuantSeq and found this link: https://rpubs.com/chapmandu2/171024

I'll try with DESeq2 then. Thank you!

ADD REPLYlink written 6 months ago by andrebolerbarros10

Oh yeah, you should trim off the adapters and do QC, if that wasn't clear. You can do that in R, but you don't have to.

ADD REPLYlink written 6 months ago by cats_dogs20
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