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!!
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!!