thebiohub/bulkrnaseq repository overview

⁠Bulk RNA-seq Data Analysis Pipeline

A containerized workflow for transcriptome analysis of bulk RNA sequencing data, built for reproducible and scalable processing from raw reads to gene-level counts.

⁠Features

• STAR — spliced alignment and gene-level read counting
• Salmon — alignment-free transcript quantification
• Reference indexing from genome FASTA and GTF annotation
• Alignment inspection and mapping summary statistics
• Transcript-to-gene summarization with tximport

⁠Usage

docker pull thebiohub/bulkrnaseq

⁠Requirements

• Docker 20.10+
• Minimum 8GB RAM recommended
• linux/amd64 only (runs under Rosetta on Apple Silicon)

⁠Citation

If you use this workflow in your research, please cite the relevant tools:

• Dobin A et al. (2013) STAR. Bioinformatics. doi:10.1093/bioinformatics/bts635
• Patro R et al. (2017) Salmon. Nature Methods. doi:10.1038/nmeth.4197

⁠Maintained by

TheBioHub⁠