Cuffquant / Cuffnorm - Why are some feature counts exactly the same?

Question

[scottdaniel25]

Hi,

I'm getting some weird counts after aligning RNA-seq to some bacterial genomes with bowtie2 and then counting / normalizing with cuffquant / cuffnorm respectively. I'm getting something like this with some of my output:

Feature A - Species 1   4440.79
Feature B - Species 2   4440.79
Feature C - Species 3   4440.79

What I'm assuming is that Feature A, B, and C are identical so cuffquant is evenly distributing the count to each of the species. Am I correct?

As an aside: I do see that when I use something like htseq-count on this data set that I get a LOT of ambiguous reads (which I know it discards when it can't be sure of a unique alignment to one spot in the (meta)genome). This reinforces my assumption above.

Many thanks!