Question: 16S metagenomics data normalization
0
gravatar for junaidkori
23 months ago by
junaidkori0
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 • 1.2k views
ADD COMMENTlink modified 23 months ago by robert.kwapich0 • written 23 months ago by junaidkori0
0
gravatar for robert.kwapich
23 months ago by
United States/New York
robert.kwapich0 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:

http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb

and

http://qiime.org/scripts/make_rarefaction_plots.html

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 23 months ago by robert.kwapich0
2

Other methods include not rarefying: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531

ADD REPLYlink written 23 months ago by fanli.gcb660
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