Cufflinks Mask Option?

Question

[nimit.jain]

Hello

I am trying to understand the mask option in cufflinks. In particular, I am confused whether the masked transcripts are excluded from the FPKM denominator. I tried running cufflinks with and without the mask option on the same dataset and the FPKM values for my genes of interest didn't change much, leading me to believe that the masked transcripts are still factored into the FPKM denominator but perhaps not included in estimation of the fragment size distribution (based on how I created the mask file, I should have seen a difference in the FPKM values if the masked transcripts were being excluded from the FPKM denominator).

Any insights/Anybody with similar experiences?

Nimit