Acquiring DEG from mapping to two reference genomes

[deckerrg]

Hi all,

I'm looking for some insight on how to accomplish an RNA-seq experiment with two samples, each sample in two conditions and with two biological controls. The genomes are available for each of the samples (same species), so I'd like to be able to map the reads separately onto their respective genome. What I haven't figured out, is how to do the DE analysis with differently named transcripts/loci/gff...etc.

I've already run through cufflinks/cuffdiff with the data, keeping the analysis separate and matching transcript names via blast, however now I'm stuck with the transcripts' log2 fold change, but no methods of proving them statistically significant.

Any advice or literature where this has been accomplished would be very much appreciated.

Best,
Robert

[SamCurt]

You're have to realign first to the same reference, or else it's an orange-apple case.