What transcript quantification tool would you recommend for 3' prime RNA-seq?

Question

[roy.granit]

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

Answer 1

[WouterDeCoster]

Salmon has a --noLengthCorrection flag.