Beta diversity

[louisville 1]

Hi Team,

I have a question regarding beta diversity. I did the analysis for all samples but I would like to select 30 samples among the 90 samples to have beta diversity. The biome includes all 90 samples and the mapping file. I am interested in only 30 samples to be on the PCO. Also, beta diversity PCO are not publication quality figure. Any help to do it. I still use qiime 1 and I hope to move to qiime 2 soon. Thanks

Bassam

[Marco Severgnini]

Dear Bassam, I don't know if you already found how to do sample selection in the meantime, but... anyway: you could use filter_samples_from_otu_table.py (http://qiime.org/scripts/filter_samples_from_otu_table.html). You can use the script specifying the IDs of the 30 samples you are interested in and obtain a reduced version of the OTU table on which you can calculate beta-diversity and PCO.

Unfortunately, I think there is no way to increase plot resolution in QIIME (I vaguely remember it was specified somewhere in an old post in the forum) and you should export PCO coordinates and plot them in another environment (such as R).

Hope this helps,

Marco