comparing transcriptomes of two species

Question

[victoria_aleks]

Hello! :) I have an idea of comparing two related but different species in order to learn if there are differences in their expression profiles. I used the bam files after tophat2 mapping in HTSeq to generate "counts-tables" and then chose top most expressed genes and compare the data. My question would be: do I need to normilize in some way the HTSeq counts (if so, then how?) or there is no sense in that since the species are different? Thanks a lot in advance!

[Asaf]

Did you map the two libraries to different genomes? Did you have more than one condition in each strain?