/oculina_heterotrophy

Data and analyses associated with the publication Rivera and Davies (in review), on the gene expression and physiological responses of the coral Oculina arbuscula to heat challenge and starvation.

Primary LanguageR

Oculina arbuscula heterotrophy and heat stress experiment

This repo contains the data and scripts associated with the manuscript: Rivera, H.E., ..., Davies, S.W. (in review) Heat challenge elicits stronger physiological and gene expression responses than starvation in symbiotic Oculina arbuscula

Organization

The repository is separated into input files, scripts, figures, and tables folders.

The read_mapping_count_scripts folder contains all scripts that were used to:

  1. Quality filter and trim raw TagSeq RNA reads
  2. Map reads to the reference O. arbuscula and B. psygmophilum transcriptomes (see https://github.com/hrivera28/oculina_apo-sym_gene_expression)
  3. Count number of mapped reads for differential gene expression analyses

All other analyses used for the publication are in the Master_analyses_final.R script

All the input data that would be needed to run analyses is included in the input_files.Final figures and tables that are in the manuscript and supplementary data are included in the respective figures and tables folders for easy reference.