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evoDNAm_paper

This is the code associated to the following article:
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts Martina Rimoldi, Ning Wang, Jilin Zhang, Diego Villar, Duncan T. Odom, Jussi Taipale, Paul Flicek, Maša Roller bioRxiv 2022.07.21.500978; doi: https://doi.org/10.1101/2022.07.21.500978

There are 4 bash pipelines, they each run with their config file:

  • BSvsChip.sh : performs the integration of ChIPseq and WGBS data
    Usage: BSvsChip.sh [-c config file] [-s stage]
    config file: BSvsChip.config

  • Annotations.sh : generate the annotation of TFBRs with methylome fragmentation information
    Usage: Annotations.sh [-c config file ]
    [-c config file]: provide config file
    [-s stage]: if specified, it must be either "CGI", "MethFrag", "cluster"
    config file: annotations.config

  • BPR.sh : identification of clustered methylation profiles Usage: BPR.sh [-c config file] [-s stage]
    [-c config file]: provide config file
    [-s stage]: if specified, it must be either "input", "parameters", "clusters" or "features"
    config file: BPR.config

  • TFbindingDivergence.sh: performs cross species projection and annotation of TFBRs Usage: TFbindingDivergence.sh [-c configFile] [-s stage]
    [-c config]: provide config file as input
    [-s stage]: must be one of "EPO", "intersect", "CrossSpecies", "LostPeak" or "finalTables"
    -h: print this help and exit
    config file: TFbindingDivergence.config

The figures and statistics of the article are within 4 Rmarkdown files:

  • MethAtTFBRs_Fig1-2.Rmd
  • Cluster_features_fig3.Rmd
  • TFbindingDivergence_Fig4.Rmd