#sym_uptake

Scripts used in Ali et al. (in press with Coral Reefs): "Recruit symbiosis establishment and Symbiodiniaceae composition influenced by adult corals and reef sediment"

Raw data available at NCBI's Short Read Archive under accession: PRJNA454384

About the "Total script.R" file: We began with .sff files from 454 Roche sequencing output of the ITS2 region (see Ali et al. paper https://www.biorxiv.org/content/biorxiv/early/2018/09/20/421339.full.pdf for primer sequences), which we then converted to .fastq files for further analysis.

The dada2 pipeline used in our script was modified from: https://benjjneb.github.io/dada2/tutorial.html

After our analysis was complete, the dada2 authors released an ITS-specific pipeline, found here for your benefit: https://benjjneb.github.io/dada2/ITS_workflow.html

The output file from the dada2 analysis is provided in this repository ('final_OutputDADA_AllOTUs_FocusYesOnly.csv'), and further output files can be found in the Ali et al. paper supplemental data. The input files for the uptake plot ('uptakedata.csv') & heat map ('rawcountswithseq.csv') are also provided in this repository.

Please contact Nicola Kriefall [thenicolakriefall(at)gmail.com] with any questions!