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  • What next after cuffDiff - isoforms

    Dear Loyal,

    thanks for the providing cummeRbund. I am enjoying this package every bit of it.

    I have one question when it comes to isoforms.

    I see that I have 702 isoforms.


    ###########################################
    CuffGeneSet instance for 669 genes

    Slots:
    annotation
    fpkm
    repFpkm
    diff
    count
    isoforms CuffFeatureSet instance of size 701
    TSS CuffFeatureSet instance of size 675
    CDS CuffFeatureSet instance of size 682
    promoters CuffFeatureSet instance of size 669
    splicing CuffFeatureSet instance of size 675
    relCDS CuffFeatureSet instance of size 669
    #############################################

    when I visualize them in IGV, for gene especially long genes my eyeballs pain and I get hypnotized by lines, to identify which exons are different, or where exactly the splicing is different between q1 q2.

    What should one do given these 701 isoforms:
    1. How to get which exons differ between q1 vs. q2
    2. How to know if expression difference between these two isoforms.
    3. How to visually focus on exons that contributed to isoform and splicing difference.


    I tried using plotTracks. I cannot see all samples lined up for an exon difference.


    Any help to resolve this issue will be greatly appreciated.

    Thanks again.
    Adrian.

  • #2
    Sorry for bumping this message.

    Could any member please share how they are using the isofom diff list from cuffdiff. How are you identifying what exon is differing between two isoforms and how are you visualizing the exonic changes.

    thanks again.

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