Question: Does QIIME OTU Table gives idea about relative abundance?
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gravatar for Nari
2.9 years ago by
Nari870
United States
Nari870 wrote:

What does the otu table obtained from qiime suggest? Can it give relative abundance of bacteria? What does the rows and column and values signify?

For example this:

OTU Table from QIIME

sequencing • 1.6k views
ADD COMMENTlink modified 2.9 years ago by fanli.gcb650 • written 2.9 years ago by Nari870
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gravatar for fanli.gcb
2.9 years ago by
fanli.gcb650
Los Angeles, CA
fanli.gcb650 wrote:

OTU tables by themselves don't impose restrictions on what the values mean, but quoting from http://qiime.org/tutorials/working_with_biom_tables.html:

It is a matrix of counts of observations on a per-sample basis. Most commonly, the observations are OTUs or taxa, and the samples are the unit of sampling in a study

Generally in 16S sequencing, yes, these are relative abundances.

ADD COMMENTlink written 2.9 years ago by fanli.gcb650
1

Either counts or relative abundances, but these are not normalized by coverage or anything and it's not like 16S rDNA count is constant in bacteria anyways. At best, relative abundance of coverage normalized 16S copies gives a solid hint of the relative abundance of bacteria in samples..

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by 5heikki8.1k
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