Which feature ID is in which sample?


When I view my deblur table, and click “Feature Detail,” I can see the “Frequency” of the Feature [OTU?] and the “# of Samples Observed In” for the feature.
I would like to know which of my samples the feature is found in and the frequency in each. A comma-separated or tab-delineated file will do. Where can I find this or how can i make this?
In my dataset, every single Feature is only found in one sample. Does that mean, assuming no errors in assembly, that each sample’s microbiome is 100% unique?


You can export your feature table to biom-format and then see the biom format documentation for converting to tsv. This should do it:

biom convert --to-tsv -i table.biom -o table.tsv

First, you may want to use filter-features to retain only features that you are interested in.

Yes, that is what is indicated, and that is extremely suspicious.

Something must have gone wrong during processing. The most likely cause I can think of is that your barcodes are still present in your reads for some reason. You should make sure that primers and barcodes have already been removed before denoising/OTU picking (and if they are not, use cutadapt trim-paired or trim-single to remove these).

I hope that helps!

Thanks. It does look like I have barcodes in the data. I’ll deal with that in another question, since cutadapt is not working with my data.

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