Hi,
I have a 454 metagenomic sample, from which I would like to extract species frequency & diversity, among other things. I am currently using MG-RAST, with GreenGenes as my SSUrRNA reference database, 96% identity cutoff, 100 bp minimum alignment length and a e-value of 10^-5. I was wondering if anyone has some experience with doing this, and whether better parameters can be used to increase sensitivity/specificity of finding SSUrRNA in such a sample?
Thanks,
Iddo
I have a 454 metagenomic sample, from which I would like to extract species frequency & diversity, among other things. I am currently using MG-RAST, with GreenGenes as my SSUrRNA reference database, 96% identity cutoff, 100 bp minimum alignment length and a e-value of 10^-5. I was wondering if anyone has some experience with doing this, and whether better parameters can be used to increase sensitivity/specificity of finding SSUrRNA in such a sample?
Thanks,
Iddo
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