nf-core/alleleexpression

Overview

Alleleexpression is a Nextflow pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.

Features

• STAR alignment with WASP mode for allele-specific mapping
• UMI-based deduplication
• Chromosome-specific analysis with configurable chromosome selection
• Beagle phasing integration
• Phaser-based allele-specific expression analysis
• Comprehensive QC with FastQC and MultiQC reporting

Requirements

• Nextflow (>=25.04.0)
• Singularity or Docker
• Reference genome and annotation files
• Beagle reference panel and genetic map (for phasing)

With -profile docker, the phASER image must be built locally first:

docker build -t phaser:latest containers/phaser

With -profile singularity it is pulled automatically from Zenodo.

Testing

The test profile downloads a simulated dataset from Zenodo (2 Mb of GRCh38 chr11, two 1000 Genomes samples with planted allele-specific expression, plus truth tables):

nextflow run nf-core/alleleexpression -profile test,docker --outdir results

To rebuild the dataset locally, run tests/scripts/make_ase_sim_data.sh (see tests/data/ase_sim/README.md).

Pipeline steps

1. Input validation and VCF preparation
2. FastQC for raw reads
3. STAR alignment with WASP mode
4. Filtering of WASP-passing reads
5. UMI-based deduplication
6. Sorting and indexing of BAM files
7. Chromosome extraction from VCF
8. Beagle phasing
9. Phaser for haplotype-level expression
10. Phaser_gene_ae for gene-level ASE
11. ASE calling per gene: binomial or beta-binomial test (--ase_test), Benjamini-Hochberg FDR (--ase_fdr) and optional minimum effect size (--ase_min_effect); see usage
12. MultiQC report generation

Output

The pipeline organizes outputs by sample name in the specified output directory:

• fastqc/: FastQC reports
• star/: STAR alignment results
• wasp/: WASP-filtered BAM files
• umi/: UMI-deduplicated BAM files
• beagle/: Phased VCF files
• phaser/: Phaser results
• ase/: Allele-specific expression results
• multiqc/: MultiQC report

Credits

• Pipeline framework: nf-core
• Tools: FastQC, STAR, UMI-tools, samtools, bcftools, Beagle, phaser, MultiQC

Contributing

Alleleexpression is under active development and we welcome contributions! If you find a bug, have an idea to improve it, or want to help implement new features (like better sex-chromosome support), feel free to open an issue or submit a pull request.

Let’s build this together.