Luke Thompson
Luke Thompson
With conda and pip, installing the qiime base install is simple. Installation instructions for Mac OS: 1. Install [Anaconda](https://www.continuum.io/downloads#_macosx) (large download, more packages) or [Miniconda](http://conda.pydata.org/miniconda.html) (small download, fewer packages) for...
http://www.earthmicrobiome.org/protocols-and-standards/initial-qiime-processing/
Need to update. Current text from 2012: There will be four key output from the EMP: 1. Gene Atlas (GA) is a centralized repository and database for all information acquired...
New primers were introduced gradually in 2015. Here's what's different: - Barcodes are now located on the forward (515) primer to enable the usage of various reverse primer constructs to...
@rob-knight suggested: we should definitely do some blooming taxa analysis as per the Shade paper and maybe encourage Ashley to do that. Ashley Shade is at Michigan State.
Some examples to consider: - EMPO categories -- How well can we predict the EMPO category at multiple levels? (Zech did this already) - ENVO categories - Soil geography --...
@rob-knight asked: can we do any global modeling stuff with the dataset we have? May be of interest to @gilbertjack and Peter Larsen.
It would be good to have a list of driving factors we expect to be important in differentiating samples, based on previous work (e.g. Lozupone and Knight's finding about salinity)....
Which biomes or sample types are most similar to each other? If you take a new sample (or a site sampled regularly over time that is changing), which biome/sample type...
Two scripts are included here: * `verify_amplicon_type.py` -- uses the first 4 nt to guess which kind of amplicon the OTU sequences come from. Currently supports 16S, 18S, and ITS....