Better organized directory structure

[saketkc]

Maybe the pbs scripts can be separated out by moving them to a new directory called pbs, rather than have them side by side with your analysis scripts.

[bdecato]

I am not sure how to best handle this. For most figures, I have two main scripts: a shell script used on the PMD/methylation files and an R script used to generate figures from the summarized data output from the shell script.

Occasionally, the shell data wrangling requires some parallelization (e.g. calculate methylation levels in a region for all 220 methylomes). I typically write a PBS for these tasks and end my shell script by submitting that task, leaving me with a PBS, shell, and R script for each figure.

I think I should probably keep those three things together for each figure. The question is whether I should un-parallelize for the github repo in the name of simplicity for future users without a PBS-based HPC cluster.

[bdecato]

Generalized this issue to just be about improving the organization of this repo. Not sure what the solution is yet.