Metastats - OTU cut-offs

Commands in mothur
1

Hello,

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?

Thanks,

Jo

2

You can use the list.otulabels and get.otulabels commands to select the OTUs you would like included in your shared file.

http://www.mothur.org/wiki/List.otulabels
http://www.mothur.org/wiki/Get.otulabels

3

Hello,

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,

Thanks,

Jo

4

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.