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How to normalize OTU abundances in 16S-rDNA sequencing data by individual sample amount?

I have extracted and sequenced 16S-rDNA from suspended biomass collected on filters. Now I want to divide the OTU counts by the volume of water filtered for each sample, in order to abtain semi-quantitative abundance estimates. Does anyone know a reasonalble way to do it? I'm using the mothur and phyloseq. Thus far I only found the option to normalize all samples to one value. In my case, however, I have different values (volumes of filtered water) for each sample.

Thanks for any suggestions,

Yuki.

16s-rdna data analysis
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written by yuki.weber81 • yuki.weber81

have you looked into QIIME?

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written by st.ph.n st.ph.n

You can change the values of the counts matrix in the phyloseq object

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written by Asaf Asaf

1 answer

Well, I also had a look at QIIME but since this is just a side project of my PhD I think I will stick with the mothur-SOP for now.

@ Asaf: Yes I was able to change the OTU table in the phylosec object. However I had to export, change, and re-import it. But it works! Thanks!

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written by yuki.weber81 • yuki.weber81

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