Question: Finding isoform expression in RNA-Seq
0
gravatar for Whoknows
3.7 years ago by
Whoknows660
Tehran,Iran
Whoknows660 wrote:

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.

 

isoform rna-seq cufflinks tophat • 2.5k views
ADD COMMENTlink modified 3.0 years ago by andrew.j.skelton735.3k • written 3.7 years ago by Whoknows660
1
gravatar for EagleEye
3.7 years ago by
EagleEye5.7k
Sweden
EagleEye5.7k wrote:
Check this post, I have explained a method to find isoform abundance. A: How to determine alternative splicing read counts
ADD COMMENTlink written 3.7 years ago by EagleEye5.7k
1
gravatar for andrew.j.skelton73
3.0 years ago by
London
andrew.j.skelton735.3k wrote:

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. 

ADD COMMENTlink written 3.0 years ago by andrew.j.skelton735.3k

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

ADD REPLYlink written 3.0 years ago by Rob2.7k
1

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

ADD REPLYlink written 3.0 years ago by andrew.j.skelton735.3k

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

ADD REPLYlink written 3.0 years ago by Rob2.7k
0
gravatar for Whoknows
3.0 years ago by
Whoknows660
Tehran,Iran
Whoknows660 wrote:

many thanks

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Whoknows660
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