Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis

Jérôme Salignon ¹, Lluís Millan-Ariño ¹, Maxime U Garcia ²

⁰Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.

Genomics +

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May 12, 2024

View abstract on PubMed

Summary

Cactus is a user-friendly pipeline for analyzing chromatin accessibility (ATAC-Seq) and gene expression (mRNA-Seq) data. It provides comprehensive downstream analyses, making genomic insights accessible to researchers without bioinformatics expertise.

Area Of Science

Genomics
Bioinformatics
Molecular Biology

Background

Next-Generation Sequencing (NGS) costs are decreasing, increasing genomic data generation.
Downstream analysis of genomic data, particularly ATAC-Seq and mRNA-Seq, remains a significant barrier for many researchers.
Existing workflows often lack comprehensive or user-friendly downstream analysis components.

Purpose Of The Study

To develop an end-to-end pipeline, Cactus, for the integrated analysis of ATAC-Seq and mRNA-Seq data.
To provide a user-friendly and reproducible solution for non-bioinformaticians to analyze chromatin accessibility and gene expression.
To enable comprehensive downstream analyses, including differential and enrichment analyses.

Main Methods

Developed Cactus, an end-to-end pipeline using Nextflow, containers, and virtual environments for reproducibility and efficiency.
Implemented preprocessing of raw sequencing reads.
Integrated differential analysis between experimental conditions and enrichment analyses against various biological databases (motifs, ChIP-Seq sites, chromatin states, ontologies).

Main Results

Demonstrated Cactus's utility in a multi-modal and multi-species case study.
Showcased Cactus's unique capabilities compared to existing ATAC-Seq pipelines.
Validated the pipeline's ability to provide comprehensive insights from combined ATAC-Seq and mRNA-Seq data.

Conclusions

Cactus offers a quick, user-friendly, and reproducible method for analyzing chromatin accessibility and gene expression data.
The pipeline empowers researchers to gain deeper insights from multi-modal genomic data.
Cactus addresses the gap in downstream analysis for non-bioinformaticians, facilitating broader genomic research.

Keywords:

ATAC-Seq Data integration Enrichment analysis Pipeline Reproducible User-friendly mRNA-Seq

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