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  • ftan
    Junior Member
    • May 2012
    • 1
    #1

    Cuff gene and transcript IDs

    I'm new to RNA seq and I hope someone can give me some general insight into my cuffcompare output.

    My Question: Why are there are multiple cuff_gene_id and cuff_id per reference transcript? I'm trying to extract a single FPKM value per reference transcript, so I don't know how to treat multiple entries for a single gene. For example, my cuffcompare output contains multiple lines for Map4k4:

    Map4k4 Map4k4 c CUFF.155 CUFF.155.1 100 569.106817 284.553408 853.660225 378.272059 91 CUFF.155.1 5782
    Map4k4 Map4k4 c CUFF.156 CUFF.156.1 100 373909.473540 166501.815197 581317.131882 248528.926936 38 CUFF.156.1 5782
    Map4k4 Map4k4 i CUFF.157 CUFF.157.1 100 870264.340261 319860.843931 1420667.836591 578444.457660 37 CUFF.157.1 5782
    Map4k4 Map4k4 i CUFF.158 CUFF.158.1 100 870264.340261 319860.843931 1420667.836591 578444.457660 37 CUFF.158.1 5782

    Are these individual fragments that have been mapped to Map4k4 with an associated FPKM? If so, is the FPKM for Map4k4 just the sum of individual entries? Sorry, I'm new...
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