whole genome shotgun assembly

Question

[najibveto]

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.

Answer 1

[GenoMax]

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.

[najibveto]

thanks a lot, one question using the RNAseq data is it possible to annotated the genome?

[GenoMax]

Possibly but it won't happen without additional work. See this recent discussion ( Eukaryotic Genome Annotation in 2016 ) for pointers.

[najibveto]

thanks a lot but i think i need cluster computer for doing the work?