Question: Diversity Analysis From 454 Data (No 16S Amplicons)
gravatar for Iddo
9.2 years ago by
Iddo230 wrote:

So I have 454 sequences from several samples which I would like to compare. No separate 16S data was generated. What would be the best way for OTU diversity analysis? I do have MG-RAST results for these data, including GreenGenes/RDP/Silva. My concern is that the number of OTUs identified this way is rather small. And yes, I did denoise the data.

metagenomics • 2.2k views
ADD COMMENTlink modified 9.2 years ago by Casey Bergman18k • written 9.2 years ago by Iddo230

Clarification, prompted by Casey's response: yes, i only have shotgun 454. I used MG-RAST, but very few 16S reads (300-800 / sample) hit the 16S database (GreenGenes). Thresholded with a minimum length of 100, 97% ID

ADD REPLYlink written 9.2 years ago by Iddo230
gravatar for Casey Bergman
9.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

If I understand your question correctly, you have shotgun metagenomic 454 data. If so, three options spring to mind: MEGAN, CARMA and the Galaxy Metagenomics Workflow. I've had good luck running and modifying the latter, but don't have experience with the other systems. If these are on target, it would be good to know which works best for you.

ADD COMMENTlink written 9.2 years ago by Casey Bergman18k
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