Finding isoform expression in RNA-Seq
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7.4 years ago
Whoknows ▴ 890

Hi friends

I have a big problem in my project to understand gene expression among isoforms, in fact all sequences with high similarity, I know that Tophat and Cufflink can correct them, but what's the best way to distinguish expression in isoforms? And how it could be possible?

Thanks

tophat isoform RNA-Seq cufflinks • 3.9k views
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7.4 years ago
EagleEye 7.3k

Check this post, I have explained a method to find isoform abundance.

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many thanks

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6.7 years ago

If you're looking for transcript quantification and differential transcript expression, I'd consider Kallisto for the quantification (very quick), and Sleuth for modelling your differential tests.

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You might also consider Salmon or the updated Sailfish (also both very quick, and both now usable with Sleuth for modeling differential tests).

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I was going to suggest Salmon, but I'm still running through that blog post before I recommend it!

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Sure; please let me know if you have any questions or thoughts about it!

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