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,
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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