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  • 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...

  • #2
    cufflinks, specifically the cuffdiff command can do that. It would be output in the cds_exp.diff file I believe.

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    • #3
      DEXSeq too but the paper is not published yet I think

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      • #4
        Thanks for the replies!

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