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ChIP ATAC seq Reporting Specifications

Process Details

  • Name: ChIP ATAC seq Reporting
  • Process UUID: 716bf03d185c4cf49dec511262803ef2
  • Process Group: Misc.

Overview

This process generates comprehensive HTML reports for ChIP-seq and ATAC-seq analysis pipelines. It creates customized reports that include quality control metrics, peak calling results, and visualization outputs, providing researchers with a complete summary of their sequencing analysis results.

This process is implemented in Bash, which invokes R scripts for report generation using R Markdown templates.

Key Functionality

  • Pipeline-Specific Reporting: Automatically selects appropriate reporting templates (ChIPseq_Reporting.Rmd or atacseq_reporting.rmd) based on the pipeline type
  • Quality Control Integration: Incorporates FastQC outputs and various quality metrics into the final report
  • Peak Analysis Visualization: Includes peak calling results, heatmaps, and bigWig file visualizations
  • Customizable Branding: Supports institutional logos and custom CSS styling for report customization

Input/Output Specification

Inputs

Required Inputs

  • count_file
    • Description: Tab-separated values file containing count data from the analysis
    • Format: TSV

Optional Inputs

  • FastQCout

    • Description: FastQC quality control report in HTML format
    • Format: HTML

  • directory

    • Description: Directory containing analysis results and intermediate files
    • Format: Directory

  • inputTXTfile

    • Description: Text file with input parameters or metadata
    • Format: TXT

  • bigWig_file

    • Description: BigWig file containing signal coverage data
    • Format: BigWig

  • bedFile

    • Description: BED format file containing genomic intervals or peak regions
    • Format: BED

  • bamFile

    • Description: Binary Alignment Map file containing aligned sequencing reads
    • Format: BAM

  • png

    • Description: PNG image files for inclusion in the report (multiple files supported)
    • Format: PNG

  • report_theme

    • Description: CSS stylesheet for customizing report appearance
    • Format: CSS

Outputs

  • outputFileHTML
    • Description: Comprehensive HTML report containing analysis results, quality metrics, and visualizations
    • Format: HTML

References & Resources

  • Tool Documentation: Contact the team for details on ChIPseq_Reporting.R and atacseq_reporting.r