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Quantify Isoforms in RNA-Seq data

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
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updated by LayneSadler LayneSadler • written by Ankit Ankit

RSEM gives transcript level counts.

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written by Ram Ram

2 answers

Salmon is quite easy to use. You can check out the getting started documentation here (https://combine-lab.github.io/salmon/getting_started/) and the full documwntation here (https://salmon.readthedocs.io/en/latest/). 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.

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written by Rob Rob

I have written a discussion of different tools here.

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

Which is why links are not answers.

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written by LayneSadler LayneSadler

Agreed, but your comment is not helpful either. You could have added the working link with a date-stamp but you chose to just criticize instead of contribute. If you could not find a working link, you could have asked for help. Snide remarks are uncalled for.

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written by Ram Ram

You made and are continuing to make this a personal thing. Apply your remarks to your own behavior.

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written by LayneSadler LayneSadler

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