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.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
- Changed the abstract. - Moved old Fig. 2 (detailed flowchart) to the supplements). - Updated Table 1 to add ATACgraph and fix errors. - Added Fig. S1-3 showing most figures and table outputs of Cactus. - Added Fig. S6 showing genome track examples of HA-HE and LA-LE genes. - Added versions for used tools and fixed typos in names. - Clarified the utility of splitting DA results. - Added reference to a tutorial on the doc.
