The scripts in this directory can be used to recreate the results and figures from my paper, Agricultural Management Affects Root-Associated Microbiome Recruitment over Maize Development (2019). Link: https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-03-19-0016-R
Notes:
- The OTU count tables and taxonomies were generated via the hundo pipeline created by Joe Brown (https://github.com/pnnl/hundo)
- 16S and ITS refer to prokaryotic and fungal data respectively.
- There is an error in USEARCH which caused one of the fungal OTUs in the .txt file to be missing an OTU label. See "k__Fungi,p__Basidiomycota,c__Agaricomycetes,o__Agaricales,f__Inocybaceae,g__Crepidotus,s__?" in ITS_OTU.txt. This needs to be corrected by entering OTU_2583 for that taxa, as it has been in the supplied DEVITS_otu.csv file.
- Soil and Compartment refer to System and Root proximity respectively.
Feel free to email me [email protected] if you have any questions.