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Comprehensive mapping of histone modifications at DNA Double Strand Breaks deciphers repair pathway chromatin signatures.
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script/alignment
scriptR
.gitignore Initial commit Aug 7, 2018
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README.md

README.md

Comprehensive mapping of histone modifications at DNA Double Strand Breaks deciphers repair pathway chromatin signatures.

Overview

Scripts used to generate all figures from our article and some raw data, like AsiSI search motif and DSB classes (HR/NHEJ).

Data accession

Data will be available at E-MTAB-5817 (expected release date : 27 september 2018).

System requirements

Alignment

The workflow was written with snakemake (python), and need some genomic tools :

  • bwa 0.7.12-r1039.
  • samtools 1.4.
  • FastQC v0.11.5.
  • R version 3.4.0 :
    • library(Rsamtools).
    • library(GenomicAlignments).
    • library(rtracklayer).
    • library(BSgenome.Hsapiens.UCSC.hg19).

Figure generation

the scripts were written with R, and need some packages :

  • library(rtracklayer).
  • library(BSgenome.Hsapiens.UCSC.hg19).
  • library(ggplot2).
  • library(reshape2).
  • library(dplyr).
  • library(Homo.sapiens).
Script Description Figures
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
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