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.