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

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
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updated by WouterDeCoster WouterDeCoster • written by roy.granit roy.granit

1 answer

Salmon has a --noLengthCorrection flag.

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written by WouterDeCoster WouterDeCoster

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