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 (>=21.10.3)
• Singularity or Docker
• Reference genome and annotation files
• Beagle reference panel and genetic map (for phasing)

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. Extraction of ASE genes
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.