alternative splicing of RNA-Seq

[AronaldJ]

Hi,

There are mainly seven types of alternative splicing exist, which are skipped exons (SE), mutually exclusive exons (MXE), alternative 5' splice sites (A5SS), alternative 3' splice sites (A3SS), alternative first exons (AFE), alternative last exons (ALE), and retained intron (RI). I want to know which software or script can show mapping reads number for them respectively. TopHat can not do it. Other softwares, for example PASSion, MapSplice and HMMSplicer, may not do it.


Thanks for any comments in advance.

Lei

[odysseus]

Hi,
You can refer to MATS (http://rnaseq-mats.sourceforge.net/). It can automatically detect and analyze alternative splicing events corresponding to all major 5 types of alternative splicing patterns. However, in my experience, you need to check the results to use for your research.
Hope that helps.

[statsteam]

The recent version of MATS (3.X.X) can handle replicates too. It is still in beta version tho.