HRIBO

Documentation

• HRIBO
  • Introduction
  • Program flowchart
  • Requirements
  • Tools
    • miniconda3
    • snakemake
    • singularity
    • HRIBO
  • Input files
    • annotation.gff and genome.fa
    • input .fastq files
    • Sample sheet and configuration file
    • cluster.yaml
  • Output files
    • Single-file Output
    • Multi-file Output
  • Tool Parameters
  • Report
  • Example-workflow
  • References

Additional information

• Workflow configuration
  • Default workflow
  • No differential expression
  • Activating DeepRibo
    • If you run deepribo locally
    • If you run deepribo on a cluster system
  • Paired-end support
• Analysis result files
  • ORF Predictions
    • predictions_reparation.xlsx
    • predictions_reparation.gff
    • predictions_deepribo.xlsx
    • predictions_deepribo.gff
  • Quality control
    • multiqc_report.html
    • heatmap_SpearmanCorr_readCounts.pdf
    • annotation_total.xlsx
    • total_read_counts.xlsx
    • annotation_unique.xlsx
    • unique_read_counts.xlsx
  • genome-browser
    • updated_annotation.gff
    • potentialStartCodons.gff
    • potentialStopCodons.gff
    • potentialRibosomeBindingSite.gff
    • potentialAlternativeStartCodons.gff
    • BigWig coverage files
  • Differential Expression
    • riborex/<contrast>_sorted.xlsx
    • riborex/<contrast>_significant.xlsx
    • xtail/<contrast>_sorted.xlsx
    • xtail/<contrast>_significant.xlsx
    • xtail/r_<contrast>.pdf
    • xtail/fc_<contrast>.pdf
  • Metagene Analysis
    • <accession>_Z.Y_profiling.xlsx/tsv
    • <accession>_Z.Y_profiling.pdf
  • Additional output
    • samples.xlsx
    • manual.pdf
    • overview.xlsx

Example

• Example workflow
  • Setup
  • Retrieve and prepare input files
    • Annotation and genome files
    • .fastq 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
  • Results
  • Runtime
  • References
• Extended workflow
  • Setup
  • Retrieve and prepare input files
    • Annotation and genome files
    • .fastq 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
  • Results
  • Runtime
  • References

FAQ

• Frequently asked questions
  • Q: When using singularity I get ERROR  : Failed to set effective UID to 0.