I need to do RNA-seq comparison between a few species of fish that are not in the UCSC genome browser (bluefin tuna, red sea bream, and torafugu putter fish). Normally, I'd first run tophat and obtain the reference files it requires (GTF and assembly for bowtie) from UCSC. However, these fish species are not yet in UCSC as tuna for example has only recently been sequenced and I haven't yet found an assembly for Pagrus major (sea bream).
I just got this project today and I'm trying to think of how I can make progress. For example, I was thinking of collecting all the known information from NCBI and creating partial GTF and assembly files myself from these. Do you know of a better way to go about it?
Thanks a lot.
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