Question: Extraction of splicing events and their quantification
0
gravatar for Anil Kesarwani
4.6 years ago by
United States
Anil Kesarwani80 wrote:

Hi,

I am using cuffdiff for the analysis of differential expression of isoforms and genes. I was wondering if cuffdiff offers any option to extract different types of alternative splicing events for example, exon inclusion or skip, intron retention, alt. 5’ and 3’ splice site selection etc, and quantify the region covering these events instead of whole isoform. I will highly appreciate if some one could guide me in this regard.

Thanks a lot.
 

rna-seq tool cuffdiff • 2.0k views
ADD COMMENTlink modified 4.6 years ago by EagleEye6.2k • written 4.6 years ago by Anil Kesarwani80
4

Cuffdiff will provide information at the isoform level. The specific events (exon inclusion or skip, intron retention, alt. 5’ and 3’ site selection etc) you are talking about can be analyzed using MATS or MISO. 

ADD REPLYlink written 4.6 years ago by Ashutosh Pandey11k
0
gravatar for EagleEye
4.6 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Have a look at this post:

How to determine alternative splicing read counts

 

ADD COMMENTlink written 4.6 years ago by EagleEye6.2k
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