Comprehensive mapping of histone modifications at DNA Double Strand Breaks deciphers repair pathway chromatin signatures.
Scripts used to generate all figures from our article and some raw data, like AsiSI search motif and DSB classes (HR/NHEJ).
Data will be available at E-MTAB-5817 (expected release date : 27 september 2018).
The workflow was written with snakemake (python), and need some genomic tools :
R version 3.4.0:
the scripts were written with
R, and need some packages :
|get_asi_location.R||Search AsiSI motif across genome.|
|get_repair_classes.R||Compute HR and NHEJ classes based on RAD51/XRCC4 and RAD51/Lig4 ratios.|
|index_BLESS.R||Plot sorted BLESS value for each AsiSI location.||Figure S1B|
|make_bamcompare_profile.R||Plot LogRatio coverage for given bigwig.||Figures 2B,3B,6B,S2D|
|make_boxplot.R||Plot the distribution for one/two bigwig with one/two bed.||Figures 1C,4B,6C,7B,7E,S4E|
|make_circle_plot.R||Compute and plot enrichment for HR sites for several windows in multiple bigwigs.||Figures 4F,S5E|
|make_heatmap_sorted.R||Plot sorted heatmap for given bigwig.||Figures 1B,4C,7D,S4D,S6C|
|make_jitter_plot.R||Plot a jittered distribution for a given bigwig with one bed file.||Figure S1D|
|make_log_boxplot.R||Plot the log ratio distribution of multiple bigwigs for one bed file.||Figures 2A, 3A, 5A, 5B|
|make_profile.R||Plot average profile for a given bigwig with one bed file.||Figures 1D,2B,4A,4D,6B,7C,S6A,S6F|
|make_profil_gene_cat.R||Plot average profile for multiple bigwig over human genes sorted by expression level||Figure S2B|
|make_vs_boxplot.R||Plot the distribution of multiple bigwigs for two bed files||Figures 4E,S5D|