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  • Same annotation file but different results

    Hi All,
    I just got problem with my fpkm calculation calculated by cufflink.
    I used the same annotation.gtf file as a reference(- G) and calculated several samples: A ,B ,C..
    Sample C use :--library-type fr-secondstrand Sample A, B use:fr-unstranded (default). I found that there are some genes in annotation file but miss in sample A final gene fpkmtracking. Moreover, the final genes item in fpkmtracking files of A B are same (still missed some genes ), but the final gene item in C are somewhat different from A and B. Less than 10 items, I am worried about my calculation. Ps: The skip.gtf is empty.
    Thank you for your help!!
    Last edited by EricHole; 08-07-2013, 07:00 AM.

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