hello i have the genome of fathead minnow as whole genome shotgun http://www.ncbi.nlm.nih.gov/genome/?term=fathead%20minnow and i want to assembly this genome so i could use it for my RNA seq mapping. is there any protocol or tutorial to do the assembly? thanks for your help.
Genome on the page linked is already assembled (to some extent, those are not raw reads). There are putative exons in the gff file though they are not annotated/functionally identified. So combining the two you should be able to do mapping of your RNAseq data.
If you have enough RNASeq data then you could look into assembling a de novo transcriptome with something like Trinity.