Question: 16S metagenomics data normalization
gravatar for junaidkori
2.6 years ago by
junaidkori0 wrote:

I have 16S amplicon metagenomics data i want to normalize my reads because number of reads varies between different samples. Can any body help me.

sequencing sequence R genome • 1.6k views
ADD COMMENTlink modified 2.6 years ago by robert.kwapich10 • written 2.6 years ago by junaidkori0
gravatar for robert.kwapich
2.6 years ago by
United States/New York
robert.kwapich10 wrote:

If you use QIIME then you could summarize your biom table, and choose appropriate depth through '-e' parameter in core diversity analyses. This accounts for differences in depth between samples. To choose this value you could simply create a rarefaction plot again in QIIME.

Just read on:


I usually sumamrize table and take the "sensible" lowest value. I.e. if the values are more or less for ex. 1000, and there is one around 150, I choose 1000, therefore excluding a particularly shallow sample and ensuring further normalization.

There may be other methods though.

ADD COMMENTlink written 2.6 years ago by robert.kwapich10

Other methods include not rarefying:

ADD REPLYlink written 2.6 years ago by fanli.gcb690
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