Question: whole genome shotgun assembly
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gravatar for najibveto
3.6 years ago by
najibveto40
Korea, Republic Of
najibveto40 wrote:

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.

assembly genome • 943 views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by najibveto40
0
gravatar for genomax
3.6 years ago by
genomax72k
United States
genomax72k wrote:

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.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by genomax72k

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

ADD REPLYlink written 3.6 years ago by najibveto40

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

ADD REPLYlink written 3.6 years ago by genomax72k

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

ADD REPLYlink written 3.6 years ago by najibveto40
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