Account for truncated empirical distribution in effective transcript length calculation#32
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Account for truncated empirical distribution in effective transcript length calculation
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I noticed a lot of variability in the FPKM estimates for some relatively short isoforms when I would perturb the input BAM a little bit. (Note: the way I would perturb the BAM would affect empirical read/fragment length distributions somewhat.) I traced the variability to the transcript's
effective_lengthand eventually to here.For the affected gene(s)
effective_lengthwas calculated as being less than 1, which was puzzling, and would vary a lot (in relative terms, not in absolute) when input was perturbed. I think this pull request is the fix: the effective length calculation is using thepdfmember of theEmpDistclass, but should be usingnpdfbecause it's considering a truncated version of the emp. dist.