Shared file with taxonomy names for otus

Commands in mothur
1

Hi,

I wonder if there is a way to include the taxonomy names for otu (found in .taxonomy file) when using the make.shared command. So, instead of ‘Otu0001’ to ‘Otu0500’ labeling the otus, i have the genus or family names.

Thanks,
Soon

2

Doesn’t do exactly what you want but if you want to combine the shared file information with the taxonomy file information you can look at create.database.

Cheers
Richard

3

I don’t think this is something that mothur allows you do to directly in mothur, because it’s possible (or common) to have multiple OTUs with the same classification so you would lose your unique OTU identifiers.

What I usually do is to just import the shared file and cons.taxonomy file into Excel or R. Since in both cases the data is sorted by OTU number you can line them up next to each other effortlessly and then analyse the data from there.

4

I see. That makes sense. Thanks.