Welcome to piquant’s documentation

piquant is a pipeline to help assess the accuracy of quantification of transcripts from RNA-sequencing data.

Contents:

• Introduction
• Overview
  • Simulate reads
  • Quantify transcripts
  • Assess quantification accuracy
  • Requirements
• Installation
• piquant commands
  • Common options
  • Prepare read directories (prepare_read_dirs)
  • Create reads (create_reads)
  • Check reads were successfully created (check_reads)
  • Prepare quantification directories (prepare_quant_dirs)
  • Prepare for quantification (prequantify)
  • Perform quantification (quantify)
  • Check quantification was successfully completed (check_quant)
  • Analyse quantification results (analyse_runs)
• Simulating reads
  • Create expression profiles
  • Calculate required number of reads
  • Simulate reads
  • Check reads
  • Join and shuffle reads
  • Fix strandedness
  • Apply sequence bias
  • Finalise output files
• Quantifying expression
  • Preparing for quantification
  • Performing quantification
  • Assessing quantification accuracy
• Quantification tools
  • Cufflinks
  • RSEM
  • eXpress
  • Sailfish
• Assessing quantification performance
  • Statistics
  • Transcript classifiers
  • Resource usage statistics
  • Assessment of a single quantification run
  • Assessment of multiple quantification runs
• Typical pipeline usage
  • 1. Create output directory and write parameters file
  • 2. Prepare read directories
  • 3. Create reads
  • 4. Check reads
  • 5. Prepare quantification directories
  • 6. Perform prequantification steps
  • 7. Quantify transcripts
  • 8. Check quantification
  • 9. Analyse quantification runs
• Support scripts
  • Analyse a single quantification run
  • Assemble data for a single quantification run
  • Calculate reads required for sequencing depth
  • Calculate unique transcript sequence
  • Count transcripts for genes
  • Fix antisense reads
  • Randomise read strands
  • Simulate sequence bias in reads
• Extending piquant
  • Adding a new quantifier
  • Adding a new statistic
  • Adding a new transcript classifier
• References