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Old 09-05-2011, 11:00 AM   #1
gfmgfm
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Default detecting alternative splicing in RNA-seq

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...
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Old 09-05-2011, 12:37 PM   #2
dpryan
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cufflinks, specifically the cuffdiff command can do that. It would be output in the cds_exp.diff file I believe.
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Old 09-05-2011, 11:23 PM   #3
Jane M
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DEXSeq too but the paper is not published yet I think
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Old 09-05-2011, 11:24 PM   #4
gfmgfm
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Thanks for the replies!
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