README.md

PineBiomeDataPaper

Scripts and files associated with the PineBiome project data paper "Metabarcode and transcriptome datasets of Pinus sylvestris to assess fungal phyllosphere and disease dynamics".

Information on the background of the study can be found at https://www.hutton.ac.uk/project/pinebiome/.

Folder layout

There are two main folders:

1. Metabarcoding => scripts, plots and data related to the ITS metabarcoding of the tree needles.
2. RNA_data => scripts and data related to the transcriptomic libraries of the tree needles.

Minimally processed OTU tables can be found in /Metabarcoding/Data/OTU_tables. These are available as tsv files:

• T1_ITS_min_clean_OTU_table.tsv
• T2_ITS_min_clean_OTU_table.tsv
• T3_ITS_min_clean_OTU_table.tsv

or can be imported directly into R from the rds objects:

• T1_ITS_min_clean_OTU.rds
• T2_ITS_min_clean_OTU.rds
• T3_ITS_min_clean_OTU.rds

OTU are named by the feature hashes from the qiime pipeline. Relevant taxonomic information for these is included in the rds object or can be cross referenced with the "seqs-and-taxonomy" tables:

• seqs-and-taxonomy_T1_ITS.tsv
• seqs-and-taxonomy_T2_ITS.tsv
• seqs-and-taxonomy_T3_ITS.tsv

License

Data

All proccessed datasets (including OTU tables) are released under CC BY 4.0.

Code

All scripts are released under the MIT License.