14 months ago by
If they are closely related genomes, it might be worth considering an RNA-Seq assembly from a related genomic alignment (using an algorithm like cufflinks)? If so, it would probably be good to have multiple samples (where I think the cuffmerge assembly is probably better than any of the individual sample assemblies).
If you have genomic sequence, you could also try using a program like MAKER (where you can provide RNA-Seq data in the annotation process). However, that may take a while for a whole genome sequence (particularly if it is a vertebrate genome).
Otherwise, I sometimes use Oases (or maybe even Velvet contigs) for RNA-Seq de novo assembly, but I would usually be assembling partial transcript sequences (most likely, for a fraction of the total transcripts in any sample). In other words, I would have some concerns about using that assembly for quantification. However, if there is a set of RefSeq sequences for your organism (I would guess from ESTs, and other sources), that may be the best option for transcript quantification.