This code repo hosts scripts and analysis protocols used to generate results that are reported in our study: Systematic comparison of experimental assays and analytical pipelines for identification of active ­­­­enhancers genome-wide

Structure of this repo

Protocols

This folder stores major protocols/pipelines that we used to analyze sequencing data. Files are in json format; they are structured as follows:

• name
• description
• step: a list of steps in this protocol/pipeline
  • step_order: the order of current step in this protocol
  • software
  • parameter
• reference: a dictionary of predefined variables that are referred to in this protocol
  • key: name of the reference
  • value: description about this reference

Analysis

Scripts that we used to analyze data generated from protocols and produce aggregated files for downstream plotting.

• assay_sensitivity.py: Analysis about assays' sensitivity in detecting eRNAs.
• assay_specificity.py:
  • Analysis about factors which affect assays' sensitivity.
  • Signal-to-noise ratio.
  • False discovery rates.
• cross_analysis_via_read_distribution.py: Analysis about the effects of rRNA.
• tools_resolution_robustness.py: Analysis about tools' applicability to different assays, resolution, and robustness.
• tools_sensitivity_specificity.py: Generate ROCs for different tools
• compendium.py: Gather summaries about the compendium
• utils.py: misc functions that are used in multiple modules
• utils_roc.py: python classes for ROC profilers

Software

To incorporate previously published tools into our pipeline, sometimes we have to modify these tools a little bit. We put all our modifications in this folder.