HRIBO

Documentation

• HRIBO
  • Introduction
  • Requirements
  • Tools
    • miniconda3 or miniforge3
    • HRIBO
    • snakemake
  • 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
  • Biology Settings
    • adapter sequence
    • genome file
    • annotation file
    • sample sheet
    • alternative start codons
  • Differential Expression Settings
    • differentialexpression
    • features
    • contrasts
    • adjusted pvalue cutoff
    • log2 fold change cutoff
  • ORF predictions
  • Read statistics Settings
  • Metagene Profiling Settings
    • Positions outside of the ORF
    • Positions inside of the ORF
    • Filtering Methods
    • Neighboring Genes Distance
    • RPKM Threshold
    • Length Cutoff
    • Mapping Methods
    • Read Lengths:
    • Normalization Methods
    • Output Formats
    • PlotlyJS
    • Colors
    • workflow
  • 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
    • deltate/<contrast>_sorted.xlsx
    • riborex/<contrast>_sorted.xlsx
    • xtail/<contrast>_sorted.xlsx
    • xtail/r_<contrast>.pdf
    • xtail/fc_<contrast>.pdf
    • output tables
  • Metagene Profiling Analysis
  • Additional output
    • samples.xlsx
    • manual.pdf
    • overview.xlsx
• Metagene profiling
  • What is metagene profiling?
  • Metagene output
  • Example output

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.