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
- 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
- Quantifying expression
- Quantification tools
- Assessing quantification performance
- Typical pipeline usage
- Support scripts
- Extending piquant
- References