Quantify Isoforms in RNA-Seq data
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12 months ago
Ankit ▴ 320

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 • 597 views
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RSEM gives transcript level counts.

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Entering edit mode
12 months ago
Rob 5.0k

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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Entering edit mode
12 months ago

I have written a discussion of different tools here.

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