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-   -   16S metagenomics, how much data needed? (http://seqanswers.com/forums/showthread.php?t=19877)

Gorbenzer 05-08-2012 08:30 AM

16S metagenomics, how much data needed?
 
Hi everyone,
i'm starting a 16S metagenomic analysis using Ion Torrent sequencer...

We need to decide what chip is better to use...

314 that gives around 40Mbp of 200bp data?
316 that gives aroung 200Mbp of 200bp data?
318 that gives around 1Gbp of 200bp data?


How much data is usually required for a good rapresentation of a sample microbial 16S population?

Thanks to everyone that will help :)

Jean 05-10-2012 10:25 AM

It depends on what the population is (how diverse for example), and how "deep" you want to sequence (do you care about rare bugs?)

Gorbenzer 05-11-2012 12:43 AM

Hi,
we need to evaluate intestinal microbiota from fecal samples, so quite high complexity... and identify rare bugs would be appreciated.

I can't find any paper about 16S metagenomics based on Ion Torrent PGM and having an idea of the amount of data needed would help us to reduce the number of runs (and the amount of money) needed to find the best settings.

Thank you for your help.

gringer 05-13-2012 06:43 PM

Quote:

we need to evaluate intestinal microbiota from fecal samples, so quite high complexity... and identify rare bugs would be appreciated.
In that case, the general rule of thumb is "as much data as possible given the money and time constraints". That's probably going to be the 318 unless there's a much greater chance of a failed run due to a newer system.


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