Exploring Data in QIIME

This is a second tutorial on QIIME primarily intended for students who have already completed the overview tutorial and feel comfortable (and hopefully excited!) to do some of their own analysis.  The idea here is for you to have a chance to try out as many QIIME features as you wish with a full-sized data set.


The Data Set

Here is a new data set for you to download. It came from this paper on microbial communities in nine anaerobic digesters treating brewery waste water. For each of the nine digesters, there is a one-year time series. In the mapping file you will find some accompanying data on environmental conditions as well as digester performance that you may find useful. 

I've already done the initial drudgery of processing the sequences. The following workflow steps are done:

Basically, it's the equivalent of up-to-and-including the pick_otus_through_otu_table.py workflow script.

Update: To be compatible with the latest QIIME file formats, I added a biom format OTU table. I also left the old text format OTU table in there to make it easier to open it up in a spreadsheet.

Your Challenge

Find three interesting trends in these data!  There are lots of places to look, and I'm not going to be judgemental about what you think is interesting. We reported a couple things in that paper, but there are TONS of other random interesting things hiding in those data. 

Some Ideas to Get Started With

There are lots of possible things to look into. Are there any aspects of the community related to the conditions or performance of the reactors? How would you characterize the dynamics of the communities over time? How are different communities structured differently?

Enjoy!  In the spirit of inquiry-based learning, I haven't tried half of those suggestions up there. Anyway, I'm sure most of the stuff you end up doing will be new and interesting. Discover!