I am fairly new to this sort of analysis, and have a question - I am picking up a project where they are comparing expression in two fairly closely related nematode genera. We have RNASeq (Illumina) data from the two taxa. When the project was begun, only one of the worms had a published genome. They used Tophat/Cufflinks with that genome to analyze the RNASeq data for both genera.
It seems, at least to my novice eyes, that using the reference genome of one taxon to analyze could be problematic - is Tophat able to map reads from one taxon to the genome of another correctly?
There is now a genome for the second taxon, and I can use that to map the reads in Tophat, but how, then, would I compare the output of the two taxa, to find genes that are differentially expressed? Is it possible to build a reference that combines the genomes of both taxa, and somehow pulls orthologs that are found in both?
Any help is appreciated!