crispr-screens

Experimental considerations

  • Model system
  • sgRNA library selection
  • sgRNA library transduction and representation
  • Sample comparisons
  • References

Installion of required software

  • Conda
  • Snakemake
  • Apptainer
  • Snakefetch
  • Obtaining workflow code

Workflow usage

  • Preparing analysis data directory
  • Experiment meta data
  • FASTQ trimming
  • BAGEL2 analysis
  • MAGeCK analysis
  • drugZ analysis
  • CRISPRcleanR
  • Setup global Snakemake profile
  • Dry-run on experimental data
  • Execution of workflow
  • Report of analysis

Protocols

  • Protocols
  • References

About

  • About crispr-screens
  • Citation

Source code

  • Reporting issues
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