Hello new here, and to bioinformatics! RAD data

[cecrobinson86]

Hi, my name is Cory and I'm working with some RADseq data, that I've just recieved... or I should say attempting to work with. I would greatly appreciate any advice on tutorials for GO annotation, and how to deal with BLAST results... I feel very in over my head as my background is in Marine Biology

Cheers folks!! Looking forward to reading up!

[JackieBadger]

Stack tutorials: http://www.simison.com/brian/Illumin...s_notes.html#1
BLAST2GO for blast and annotation: http://www.blast2go.com/b2ghome

[SNPsaurus]

Hi Cory,

I'm trying to figure out how the RAD data connects to GO annotation. Are you taking the RAD tag sequences, BLASTing to a related reference, then trying to connect the BLAST hits to known GO annotation? And are you doing this to try to order your RAD tags based on synteny with the reference?

Most RAD tags won't overlap with a gene, but rather be in intergenic regions that will be difficult to annotate. My colleague John Postlethwait used RAD PE contigs to try to connect more RAD tags to genes, but the same approach could be used on the regular RAD tags as well (http://www.genetics.org/content/188/4/799.full) and give you an idea on a workflow.