What transcript quantification tool would you recommend for 3' prime RNA-seq?
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5.5 years ago
roy.granit ▴ 880

I've searched around and could not find (possibly missed) advice on which transcript quantification tool is well suited for 3' prime RNA-seq lib?

I've considered using Salmon, but I'm not sure if it will correct for transcript length which is expected to be only a small part of the transcript

Would be glad to hear your inputs.

Thanks!

P.S. downstream I intend to use DEseq2

RNA-Seq transcript quantification salmon • 1.2k views
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Entering edit mode
5.5 years ago

Salmon has a --noLengthCorrection flag.

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