Hi,
I'm an RNAseq guy who has just started a Genome project. Unfortunately its a baptism of fire since the subject is a symbiosis. I have an assembly using Edena (2K contigs) presumably including both fungal and bacterial fragments.
I have a feeling a meta genomics approach to analysis may be useful.
So what next? Genotype/find the nearest relative by 16s? If so what "generic" 16s should I use to pull out my species 16s (I guess may be more than two things in there).
Is there an established strategy to assemble both separately? Should I go back to the reads and try to separate them prior to an assembly?
Any help appreciated.
FGP
I'm an RNAseq guy who has just started a Genome project. Unfortunately its a baptism of fire since the subject is a symbiosis. I have an assembly using Edena (2K contigs) presumably including both fungal and bacterial fragments.
I have a feeling a meta genomics approach to analysis may be useful.
So what next? Genotype/find the nearest relative by 16s? If so what "generic" 16s should I use to pull out my species 16s (I guess may be more than two things in there).
Is there an established strategy to assemble both separately? Should I go back to the reads and try to separate them prior to an assembly?
Any help appreciated.
FGP
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