Data and code

This folder contains all the data and analysis scripts used in the publication. For fastq files used to generate the ASV tables they have been deposited in BioProjects PRJEB52183, PRJEB62148, and ZZ. For ease, however, they are all available in this Dropbox link with all the control wells.Files included here are:merged_data_44_blast_ordered - the dataset used in this analysisCF_interaction_code_shared - R code to recreate the analysis and figures presented in the manuscriptCF_interaction_code_initial_clean_shared - R code for the initial clean-up and merging of the ASV, metadata, and taxa data sets. Culminates in the creation of "merged_data_44_blast_ordered.csv".DATASET_unclean - contains all of the metadata for the samples used.taxa_44_blast - contains all of the ASV sequences and taxa alignments, after manually blasting the unassigned sequences.ASV_table_44 - contains all the read data for the samples and sequence.