Finding isoform expression in RNA-Seq

Question

[Whoknows]

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

Answer 1

[EagleEye]

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

[Whoknows]

many thanks

Answer 2

[andrew.j.skelton73]

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.

[Rob]

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

[andrew.j.skelton73]

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

[Rob]

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