Alexandra Bartlett: Streamlining RNA-Seq Data Analysis with rnaseq-reports

Alexandra Bartlett - Bioinformatician II at Harvard Chan Bioinformatics Core RNA sequencing (RNA-Seq) has revolutionized the field of genomics and molecular biology, providing a comprehensive tool for characterizing and quantifying the transcriptome. Its ability to capture a snapshot of the entire range of RNA molecules allows researchers to understand gene expression patterns, discover novel transcripts, and identify alternative splicing events, generating insights into the molecular underpinnings of diseases and developmental processes. The nf-core/rnaseq pipeline is a robust and standardized workflow designed for the comprehensive analysis of RNA sequencing data. Using the Nextflow framework and community-driven standards and best practices, the pipeline automates the complex processes of quality control, alignment, and quantification. However, after completing this rigorous pre-processing, researchers frequently face challenges with applying downstream data analysis methods in ways consistent with their unique experimental designs and datasets. The rnaseq-reports project aims to use basic outputs from the nf-core/rnaseq pipeline to facilitate decision-making for downstream analyses, such as quality control, differential expression, comparative, and functional analyses. It provides customizable templates and application-focused guidelines for using various relevant packages and statistical techniques that are recognized as best practices by different bioinformatics communities. The templates assist in choosing the right analysis strategy and generating reproducible, easily digestible reports for presentation and discussion, enabling researchers to concentrate on data interpretation and gaining valuable biological insights. Nextflow Summit Boston 2025 https://summit.nextflow.io/2025/boston/agenda/streamlining-rna-seq-data-analysis-with-rnaseq-reports/