Question: Quantify Isoforms in RNA-Seq data
gravatar for Ankit
8 weeks ago by
Ankit160 wrote:

Hi everyone,

I know this question has been asked multiple times in other posts, but I am still not clear.

I want to quantify counts for each isoforms. I am not sure how it will be possible specially for overlapping transcripts.

I think featurecounts is not good for isoform quantitation. I never used salmon or kallisto. So may be if someone has a prior experience or a thought process, please let me know.

Thank you

rna-seq isoforms • 212 views
ADD COMMENTlink modified 7 weeks ago by kristoffer.vittingseerup3.5k • written 8 weeks ago by Ankit160

RSEM gives transcript level counts.

ADD REPLYlink written 8 weeks ago by _r_am32k
gravatar for Rob
8 weeks ago by
United States
Rob4.6k wrote:

Salmon is quite easy to use. You can check out the getting started documentation here ( and the full documwntation here ( If you have any questions where you don't find answers here or in the FAQ, feel free to raise an issue over on the github page.

ADD COMMENTlink written 8 weeks ago by Rob4.6k
gravatar for kristoffer.vittingseerup
7 weeks ago by
European Union
kristoffer.vittingseerup3.5k wrote:

I have written a discussion of different tools here.

ADD COMMENTlink written 7 weeks ago by kristoffer.vittingseerup3.5k
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