uORF-Tools

Documentation

• uORF-Tools
  • Introduction
  • Program flowchart
  • Directory table
  • Input/Output Files
    • uORFs_regulation.tsv
  • Tool Parameters
  • Requirements
  • Tools
    • miniconda3
    • snakemake
    • uORF-Tools
  • Input files
    • genome.fa and annotation.gtf
    • input .bam files
    • Sample sheet and configuration file
    • cluster.yaml
  • Example-workflow
  • Preprocessing-workflow
  • References

Examples

• Example workflow
  • Setup
  • Retrieve and prepare input files
    • Annotation and genome files
    • .bam files
    • Sample sheet and configuration file
  • Running the workflow
    • Run the workflow locally
    • Run Snakemake in a cluster environment
    • Example: Run Snakemake in a cluster environment
    • Report
  • References
• Preprocessing workflow
  • Setup
  • Retrieve and prepare input files
    • Annotation and genome files
    • Fastq files
      • European Nucleotide Archive (ENA)
    • Sample sheet and configuration file
  • Running the workflow
    • Information about processing parameters
    • Run the workflow locally
    • Run Snakemake in a cluster environment
    • Example: Run Snakemake in a cluster environment