Quantify Isoforms in RNA-Seq data

Question

[Ankit]

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

[Ram]

RSEM gives transcript level counts.

Answer 1

[Rob]

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.

Answer 2

[Kristoffer Vitting-Seerup]

I have written a discussion of different tools here.

[LayneSadler]

Page not found

[Ram]

That's because it's a 3 year old link on a constantly changing website. If you dug around a little - 5 minutes of effort, you'd find it here: https://bioconductor.org/packages/release/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-quantification-tools-should-i-use

[LayneSadler]

Which is why links are not answers.

[Ram]

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.

[LayneSadler]

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