rlooper-plasmids

Basically just a refined version of this repo. Main changes are

Runs on new HPC cluster; Franklin
Uses Snakemake parameter exploration functions to allow for easily setting large number of run parameters (Do this by changing values in resources/rlooper_params.tsv
Output filepaths include parameters used in each run
Additional python scripts to process wig bp predictions into tsv files with the parameters used in each run in long format for easy plotting with ggplot2
Runs on any sequence (in theory) with a correct R-loop fasta header that is located in the resources/sequences directory

Cloning this repo

Remember to add the submodules to the repo when cloning or just do it after forgetting like me using this command

git submodule update --init

If this is not done then the workflow will fail to compile R-looper and will not run.