question about RNA-seq in hybridized animals

[boyzoe]

Hi! Guys!
I have RNA-seq data of one hybrid and its parents (father and mother). I wanna to align transcript sequences of these three samples. I don't know if there is any appropriate tools for this work. By the way, genome of these species remain un-sequenced, so any method needs genome sequence is not feasible.

Thanks, guys!

[Hyeshik Chang]

How about trying de novo assembly of the sequence reads?

See: http://bioinformatics.oxfordjournals...ull/25/21/2872

[jwfoley]

Your situation sounds difficult. You probably should have thought about this part before you generated the data, since it's not clear if you can use them now.

De novo assembly is possible, even with short reads as in that paper, but you need a lot of coverage. A few Solexa lanes would be insufficient for a mammalian genome, but this might work if your genome is much smaller than mammalian or if you have 200 million reads like the authors did.

If you hadn't already done your experiment, I would have suggested you sequence either the genome or the transcriptome first, using a system with long reads like 454. Perhaps you can align to a reference genome from a closely related species.