bdecato/pmd_paper_scripts

A repository containing code, data, and resource links for the publication "Characterization of universal features of partially methylated domains across tissues and species"

Hi there 👋

pmd_paper_scripts's Issues

Better organized directory structure

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.

Specify path to binary

One Line 21, the
binary location can be specified through a parameter instead of hard coded path.

Take prefix for outputting pdfs

One Line 13, you could take a prefix four outputting the pdfs rather than a hardcoded path.

Swap every qsub script to slurm

HPC changed their job scheduler to slurm. If I want to quickly reproduce my findings (which I will have to do in the coming weeks), each PBS script in this repo needs to be converted to a slurm script.

Print help message for missing arguments in download_methcouts

https://github.com/bdecato/PMD_Paper_Scripts/blob/master/downsample_methcounts.py#L82
should print a help message describing what input it expects.