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mageckCount Specifications

Process Details

  • Name: mageckCount
  • Process UUID: 6pKk7iyrPDDUR0RBfSOGujZUns22Gi
  • Process Group: Crispr

Overview

The mageckCount process performs read counting for CRISPR screening data using the MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) toolkit. This process counts sgRNA reads from FASTQ sequencing files against a provided library, generating count tables and quality control reports essential for downstream CRISPR screen analysis.

This process is implemented in Bash, which invokes R scripts for report generation and data visualization.

Key Functionality

  • Read Counting: Counts sgRNA reads from FASTQ files using the MAGeCK count algorithm
  • Quality Control: Generates comprehensive PDF and HTML reports with read distribution statistics and quality metrics
  • Sample Labeling: Processes multiple samples with user-defined labels for downstream comparison
  • Report Generation: Creates interactive HTML reports using R Markdown with statistical summaries and visualizations

Input/Output Specification

Inputs

Required Inputs

  • txtFile (Library File)

    • Description: sgRNA library file containing guide sequences and target gene annotations
    • Format: TXT

  • text (Sample Labels)

    • Description: Comma-separated sample labels for identifying treatment conditions
    • Format: Text

  • text (Count Prefix)

    • Description: Output file prefix for naming result files
    • Format: Text

  • reads

    • Description: FASTQ sequencing files containing sgRNA reads from CRISPR screen
    • Format: FASTQ

Outputs

  • txtFile (Count Table)

    • Description: Tab-delimited count matrix with sgRNA counts across samples
    • Format: TXT

  • outputHTML

    • Description: Interactive HTML report with quality control metrics and visualizations
    • Format: HTML

  • txtFile (Summary Statistics)

    • Description: Summary statistics file with read mapping and quality metrics
    • Format: TXT

Parameters & Settings

This process runs conditionally when the run_mageckCount parameter is set to "yes" in the pipeline configuration.

References & Resources

  • Tool Documentation: Contact the team for details on MAGeCK count module implementation
  • Related Papers: Li, W., Xu, H., Xiao, T. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol 15, 554 (2014). https://doi.org/10.1186/s13059-014-0554-4