Question: How to normalize OTU abundances in 16S-rDNA sequencing data by individual sample amount?
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gravatar for yuki.weber81
3.3 years ago by
yuki.weber8110
yuki.weber8110 wrote:

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.

data analysis 16s-rdna • 1.6k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by yuki.weber8110

have you looked into QIIME?

ADD REPLYlink written 3.3 years ago by st.ph.n2.5k

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

ADD REPLYlink written 3.3 years ago by Asaf6.5k
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gravatar for yuki.weber81
3.3 years ago by
yuki.weber8110
yuki.weber8110 wrote:

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!

ADD COMMENTlink written 3.3 years ago by yuki.weber8110
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