deep-dive

This repository is focused on taking molecular data from three experiments where integrated epigenetic analysis has already been performed, and doing a deeper dive into datasets to extract and analyze remaining points of excitement.

OSF Project Link

Follow this link to our Open Science Framework (OSF) storage directory for more easily downloadable GitHub data and storage of larger data files (i.e., genomic data).

Specific sub-efforts

D) Acropora pulchra

E) Porites evermanni

F) Pocillopora tuahiniensis

How to work in this repo

(file structure)

Top level directories are associated with each sub-effort categorized by species.

For instance:

A-Pver
B-Mcap
C-Pacu
D-Apul
E-Peve
F-Ptua

Within each top level directory there should be 3 directories:

data
code
output

For any document code it should start with a 2 number prefix (eg 01-methylation-explore.Rmd). All output from that code should be in a sub-directory of output named the same as the code. For example the output of 01-methylation-explore.Rmd would be in A-pver/output/01-methylation-explore/

Please use Relative Paths. Commit and Push often.

Links to other data types (e.g. FastQs, BAMs) can be found in the project wiki.

More

Genomes of interest

All genomes of interest can be found in our species descriptions and genomic resources wiki page.

Workflows