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