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gfmgfm 09-05-2011 12:00 PM

detecting alternative splicing in RNA-seq

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 09-05-2011 01:37 PM

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

Jane M 09-06-2011 12:23 AM

DEXSeq too but the paper is not published yet I think

gfmgfm 09-06-2011 12:24 AM

Thanks for the replies!

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