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
Docs
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v: v1.1.0
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