piquant
  • 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
 
piquant
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© Copyright 2014, Owen Dando.

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