Datasets used in this workshop

In this workshop, we will be using data from Wagner et al. (2016), a study on the effects of plant age, genotype, and environment on the bacterial microbiome of Boechera stricta, a perennial herb in the mustard family. Wagner et al. (2016) released their raw data with the article and it is available here on dryad. This is a great example of how to share your raw data!

A copy of this data is included in this site and can be downloaded from links below.

Sample metadata

A table with a sample in each row and info about the samples in each column, such as plant genotype and field site. It is a 170Kb tab-delimited text file.

SMD.txt

The OTU abundance table

This has the number of reads associated with each OTU in each sample. It is a 6Mb compressed tab-delimited text file.

otuTable97.txt.bz2

The OTU taxonomy file

This has the taxonomic classifications for each OTU. It is a 6Mb tab-delimited text file.

taxAssignments97.txt

References

Wagner, Maggie R, Derek S Lundberg, G Tijana, Susannah G Tringe, Jeffery L Dangl, and Thomas Mitchell-Olds. 2016. “Host Genotype and Age Shape the Leaf and Root Microbiomes of a Wild Perennial Plant.” Nature Communications 7: 12151. https://doi.org/10.1038/ncomms12151.

Metacoder's documentation by The Grunwald lab and the USDA Horticultural Crops Research Unit is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Based on a work at https://github.com/grunwaldlab/metacoder_documentation.