Question

DESeq2 for QuantSeq data

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andrebolerbarros ▴ 20

@andrebolerbarros-16788

Last seen 6 months ago

Portugal

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 • 1.9k views

ADD COMMENT • link updated 5.7 years ago by cats_dogs ▴ 20 • written 5.7 years ago by andrebolerbarros ▴ 20

score 1 · Answer 1 · 2019-03-27

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cats_dogs ▴ 20

@cats_dogs-15904

Last seen 5.7 years ago

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 COMMENT • link 5.7 years ago cats_dogs ▴ 20

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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 REPLY • link 5.7 years ago andrebolerbarros ▴ 20

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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 REPLY • link 5.7 years ago cats_dogs ▴ 20