Quick sequencing update:
We had to switch sequencing centers due to the sequencing instrument not working and unable to be repaired after more failed runs. I hope to the have DNA in the new center's hands this coming week and then to have data in 2-3 weeks.
Sorry again the wait...it has been one hurdle after another.
Using some old data of mostly bokashi samples, I tried to demonstrate some of the most common microbial diversity analysis we perform when starting to look at a dataset. I'll try to go more into depth on topics like alpha and beta diversity but they begin to allow us to understand very diverse and complex samples without looking at something like a bar chart with a legend that fills multiple pages.
I will try to do individual posts on some of these diversity topics, but I hope you can see that this data can go much deeper than just bar charts. Other than diversity analysis, we can also do statistical analysis to see what organisms are similar or different between samples.
I'm sure you can start to think up some of your own experiments or how you might use some of these techniques to monitor your own systems. The real key to making the most of this data is to use the "metadata," or other sample information, to better understand why one sample is more diverse than another or why some samples have similar/different communities.
If you have any questions please ask!