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