analyses Subdirectory Structure

This subdirectory hosts the output of all analyses regarding C. virginica epigenetic response to ocean acidification. Every folder houses all necessary files for a discrete analysis step in a larger pipeline. Folders follow this naming convention:

Year-Month-Date-AnalysisStep (ex. 2018-10-25-MethylKit)

The following pipelines are represented in this subdirectory:

2018-10-25-MethylKit:

• R Markdown Script for identifying DMLs and DMRs
• 2018-10-25-Loci-Analysis: Subdirectory with dendograms, PCAs, and plots depicting CpG coverage and methylation for each sample produced when identifying DMLs
• 2018-10-25-Tiling-Analysis: Subdirectory with dendograms and PCAs from tiling window analysis to identify DMRs

2018-11-01-DML-and-DMR-Analysis:

• Output from this analysis was often too large for Github and can be found in this gannet folder
• 2018-11-14-Flanking-Analysis: Subdirectory with output from bedtools flank and bedtools closest analysis