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Old 01-18-2011, 06:26 AM   #1
idoerg
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Location: Oxford, OH USA

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Default best strategy for rRNA from shotgun?

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

Last edited by idoerg; 01-18-2011 at 06:29 AM.
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Old 04-30-2011, 05:03 PM   #2
Chuckytah
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Originally Posted by idoerg View Post
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
Hello,

i'm doing a work similar, i think... but i used 80%identity cutoff, isn't right? I think if I use 96% a lot of sequences will not appear, right? 80% its good? or some will miss too?
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Old 05-01-2011, 08:12 AM   #3
idoerg
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Hello,

i'm doing a work similar, i think... but i used 80%identity cutoff, isn't right? I think if I use 96% a lot of sequences will not appear, right? 80% its good? or some will miss too?
80% for SSUrRNA is not specific enough, and basically you will be grouping all bacteria together as a single OTU
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Old 05-01-2011, 09:19 AM   #4
Chuckytah
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80% for SSUrRNA is not specific enough, and basically you will be grouping all bacteria together as a single OTU

it is not form SSurRNA it's DNA samples, from root-soil, plant. and i need to separate from plant and fungi only.
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