# Nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair

## Code for reproducible analysis

### Data
The helper script `download_sra.sh` will fetch the bam files from SRA.  Needs NCBI tools. 

### Setup
`enviroment.r` loads the required R functions and libraries. Needs to be executed first.

`nucleosome_analysis.r` generates the statistics describing the nucleosomes in each experiment.

### Figure Generation
`figure_1_5_mnase_coverage.r` generates the MNase coverage panels for Figures 1 and 5.

`figure_2_control_loci.r` generates Figure 2.

`figure_3_4_pho5_mutants.r` generates Figures 3 and 4.

`figure_5_6_nhej.r` generates Figures 5 and 6.
