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Old 06-06-2012, 04:00 PM   #1
roliwilhelm
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Question Creating "Consensus" Sequence between Reference and Mapped Reads

Hello!

I've mapped all of my Ion Torrent reads (~100bp) to a reference genome (Bradyrhizobium ORS278) and I would like to someone how splice out all the Bradyrhizobium sequence that has >97% similarity to my mapped reads. I'd like to do this because I think (now correct me if I'm wrong) that this would be a good method for comparing the genetic make-up of my env. isolate to Bradyrhizobium. I'd then take this pseudo-consensus sequence (i.e consensus of all the ORFs/genes between my unknown and the unannotated genome) and run it through a pathways identifier.

Is it possible to say: give me all the sequence from my reference genome that has > 20 x reads mapped and spit it out as its own list of homologous genes?

Or, does anyone have a different approach?

Thanks in advance,
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Old 07-23-2012, 11:09 AM   #2
nupurgupta
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Did you figure this out please?
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Old 07-23-2012, 11:21 AM   #3
roliwilhelm
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No! I have not yet figured this out, (mostly because this project is secondary to my main project), but if you or anyone else reading this thread have any input, I would be very appreciative!
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