Question: What transcript quantification tool would you recommend for 3' prime RNA-seq?
0
gravatar for roy.granit
6 months ago by
roy.granit800
Israel/LabWorm
roy.granit800 wrote:

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

ADD COMMENTlink modified 6 months ago by WouterDeCoster40k • written 6 months ago by roy.granit800
4
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster40k wrote:

Salmon has a --noLengthCorrection flag.

ADD COMMENTlink written 6 months ago by WouterDeCoster40k
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