RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting.

F1000Research
Travis L JensenJohannes B Goll

Abstract

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine via a Docker container or installation script. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage Service (S3), or at the Sequence Read Archive (SRA). RSEQREP automatically executes a series of customizable steps including reference alignment, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially expressed genes, heatmaps, co-expressed gene clusters, enriched pathways, and a series of custom visualizations. The framework outputs a file collection that includes a dynamically...Continue Reading

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Citations

Mar 27, 2019·Therapeutic Advances in Ophthalmology·Nicholas Owen, Mariya Moosajee
Apr 12, 2019·PloS One·Ravi MadduriIan Foster
Jun 5, 2021·BMC Bioinformatics·Alessandro La FerlitaAlfredo Pulvirenti
Jun 15, 2021·Nucleic Acids Research·Ashley Mae ConardErica Larschan

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Software Mentioned

Linux OS
Star
Amazon Web Services
Amazon
Google Cloud Platform
dump
RSEQREP Amazon Virtual Machine Image
Ensembl
knitr R package
Perl scripts

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