Abhinav Nellore and colleagues released a study describing a protocol and software tool for analyzing protected genomic data on a commercial cloud. Public sequencing archives like the SRA contain thousands of trillions of bases of valuable sequencing data. More than 40% of the SRA is human data protected by provisions such as dbGaP. To analyze dbGaP-protected data, researchers must typically work with IT administrators and signing officials to ensure all levels of security are implemented at their institution. This is a major obstacle, impeding reproducibility and reducing the utility of archived data.

We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol is applicable to any MapReduce tool running on Amazon Web Services. The tool, Rail-RNA v0.2, is a spliced aligner for RNA-seq data, which we demonstrate by running on 9,662 samples from the dbGaP-protected GTEx consortium dataset. These are important first steps toward making it easy for typical biomedical investigators to study protected data, regardless of their local IT resources or expertise.