{"entity": "publication", "iuid": "2f043f780fab4fd8bd86cc5b87bf739b", "timestamp": "2026-08-23T09:24:46.157Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2f043f780fab4fd8bd86cc5b87bf739b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2f043f780fab4fd8bd86cc5b87bf739b"}}, "title": "Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis.", "authors": [{"family": "Salignon", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Millan-Ari\u00f1o", "given": "Llu\u00eds", "initials": "L"}, {"family": "Garcia", "given": "Maxime U", "initials": "MU"}, {"family": "Riedel", "given": "Christian G", "initials": "CG"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Genomics", "issn": "1089-8646", "volume": "116", "issue": "4", "pages": "110858", "issn-l": "0888-7543"}, "abstract": "The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.", "doi": "10.1016/j.ygeno.2024.110858", "pmid": "38735595", "labels": [], "xrefs": [{"db": "pii", "key": "S0888-7543(24)00079-X"}], "notes": [], "created": "2026-08-21T11:31:33.635Z", "modified": "2026-08-21T11:31:33.665Z"}