I got my hands on the raw data from my colleague. It’s roughly 4 gigs of data. I am not yet ready to dive into it, but I understand more about what I’m supposed to be doing.

Atacama Tutorial

After reading more of the tutorials, I have found that the Atacama tutorial looks very similar to what my colleague is looking for. They are both paired-end reads of soil-like microbiomes. I have not walked through the whole tutorial yet, but I feel pretty confident about what to expect, especially now that I’ve watched a bunch of those microbiome videos.

Workstation Issues

I had some issues trying to run the tutorial on my older work computer, and after a quick check-in with the QIIME forum, I was able to get it to run up to the denoising step by increasing the available RAM. I also had the VirtualBox installed on my current work computer.

Right now, I’m monitoring the processing speed of to see if I think I could realistically do the full dataset that I have. On the 10% tutorial dataset, the DADA2 step took about 27 minutes on the old computer and about 14 minutes on the new one. Those data sets are about 300 megs. So the full data set is roughly similar in size to the one that I’ve got to work with. If time scales linearly, this step is going to take 2-3 hours. So this is something I may set to run at the end of the day and just come back to it the next day.

I should probably focus on finishing the tutorial, first.