This example is for the impatient (like me): running part 1 of the QIIME tutorial--checklist version.
[ UPDATE Note: the "workflow script" in the tutorial is actually easier to run than what I have here. It needs only three changes: paths to the Greengenes files (below) and changing the rep set picking method to
most_abundant, if desired. This post is about doing the workflow in such a way that the scripts are invoked individually. ]
Prerequisites (as discussed here and here)
Install and test:
Make sure you have the equivalent of this (some scripts don't seem to look at
~/bin/qiime/binis on your
From the Desktop, get the Greengenes core set data file (38 MB download link). Also get the Greengenes alignment lanemask file (download link). And get the tutorial files (download link), or do:
Make some directories:
For the next two steps, if you get an error, recheck the file extensions:
I prefer short names, so these directory and file names are different than those in the tutorial.
At this point, you could make a backup (including the huge core.txt):
Rather than do another heatmap, I thought I'd show a summary area chart
Unfortunately, it's not what we want (the graphic at top seems to be plotting the individual OTUs rather than Phyla). The example in the tutorial uses
I don't see an option for controlling the level of output in
make_otu_table.py. I'll have to investigate how to do that. Perhaps if we follow the workflow script it will turn out correctly.