Scripts and important data for "Bacterial inoculation elicits changes to the coral epigenome"
This repository contains the scripts (or references to scripts) and input files used for analyzing the epigenetic response of Pocillopora verrucosa to bacteria inoculation and heat stress in the paper "Bacterial inoculation elicits changes to the coral epigenome"
The methylation pipeline used to process samples to this point can be found at https://github.com/lyijin/working_with_dna_meth (which also contains fuller descriptions + theoretical considerations of the pipeline, and the scripts written to operate on Bismark's output)
all.filt.annot.merged.cov.gz- Methylated positions were called, filtered, and merged across all samples (explained at https://github.com/lyijin/working_with_dna_meth)
compiled_median_meths.tsv.gz- Median methylation levels were calculated on the gene level for each of the samples and compiled (explained at https://github.com/lyijin/spis_dna_meth/tree/master/bias_density_medians)
phenotype_Rscripts- Contains the R scripts used to analyze the phenotypic response of P. verrucosa to bacterial inoculation and heat stress
16S_analysis_Rscripts- Contains the R scripts used to analyze the bacterial community responses to bacterial inoculation and heat stress
methylation_Rscripts- Contains the R scripts used to analyze the gene methylation of P. verrucosa in response to bacterial inoculation and heat stress
genome_context- Contains the python scripts adapted from https://github.com/lyijin/pdae_dna_meth/tree/master/descriptive/genomic_context used to analyze the methylation levels across genes
RNAseq_Rscripts- Contains the R scripts following the sleuth pipeline (https://pachterlab.github.io/sleuth) to analyze the gene expression levels and correlate the RNA and epigenomes responses to bacterial inoculation and heat stress