detecting alternative splicing in RNA-seq

[gfmgfm]

Hello,

In RNA seq analysis - I have aligned reads to the genome and estimated the abundance of known transcripts in each sample.

In the next step I would like to find genes which their "exon usage" is different between different samples. Thanks in advance for any suggestions...

[dpryan]

cufflinks, specifically the cuffdiff command can do that. It would be output in the cds_exp.diff file I believe.

[Jane M]

DEXSeq too but the paper is not published yet I think

[gfmgfm]

Thanks for the replies!