I have 577 OTUs in my shared file. However, I would like to set a cut-off so that only a specific number of these OTUs will be tested using Metastats.
Is there a way of setting up the shared file in such a manner, so that (for arguments sake), only 100 of these OTUs will be tested and FDR corrected?
You can use the list.otulabels and get.otulabels commands to select the OTUs you would like included in your shared file.
Thank you for your reply. I have tried this using your suggestions, but I’m afraid I don’t understand how to specify which OTUs to take forward into the shared file using these 2 commands.
Any further advice would be greatly appreciated,
Perhaps you are looking for the filter.shared command, http://www.mothur.org/wiki/Filter.shared, which allows you to remove OTUs based on various criteria. Take special note of the makerare parameter which sometimes gives people trouble downstream when the rareOTUs label is included.