Analyzing gene expression, gene/ncRNA coexpression, and interactions with DNA methylation in three species of stony coral. This work builds on a completed summary of the ncRNA landscape of these species (deep-dive).
As in deep-dive, this expression/co-expression work will focus on the following three species of stony corals:
D) Acropora pulchra
E) Porites evermanni
F) Pocillopora tuahiniensis
Top level directories are associated with each sub-effort categorized by species. For instance:
D-Apul
E-Peve
F-Ptua
Within each top level directory there should be 3 directories:
data
code
output
Any document in code should start with a 2 number prefix (e.g., 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.
All genomes of interest can be found in our species descriptions and genomic resources wiki page.