These scripts and data are for the analysis of physiology (IPAM fluorometry and respirometry), transcriptome and microbiome data for the publication "Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption, and activate immune gene expression".
Bacteria 16S and RNAseq data are deposited in the NBCI SRA under BioProject PRJNA818888. Scripts used for processing bacteria 16S reads with QIIME2 are located in bash/qiime2 , and scripts used for processing 3'-tagged RNAseq reads are located in bash/tagseq. RMarkdown files used in downstream data analysis to produce the manuscript figures are located in Rmd.
The following RMarkdown files were used for the manuscript analyses:
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mtORF_haplotypes.Rmd- Analysis of mtORF sequences to determine Pocillopora host lineages -
IPAM_analysis.Rmd- Analysis of IPAM photosynthetic efficiency data -
respR_analysis.Rmd- Analysis of microplate respirometry data with respR -
phyloseq_microbiome_analysis.Rmd- Analysis of bacteria community diversity and composition -
quantseq_transcriptome_analysis.Rmd- Analysis of Pocillopora coral gene expression
