Research area: bioinformatics

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

Created on 5th March 2016

Abhinav Nellore; Christopher Wilks; Kasper D Hansen; Jeffrey T Leek; Ben Langmead;

Motivation: Public archives contain thousands of trillions of bases of valuable sequencing data. More than 40% of the Sequence Read Archive 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. Results: We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol, Rail-dbGaP, is applicable to any tool running on Amazon Web Services Elastic MapReduce. 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. The Rail-dbGaP protocol makes explicit for the first time the steps an investigator must take to develop Elastic MapReduce pipelines that analyze dbGaP-protected data in a manner compliant with NIH guidelines. Rail-RNA automates implementation of the protocol, making it easy for typical biomedical investigators to study protected RNA-seq data, regardless of their local IT resources or expertise. Availability: Rail-RNA is available from Technical details on the Rail-dbGaP protocol as well as an implementation walkthrough are available at Detailed instructions on running Rail-RNA on dbGaP-protected data using Amazon Web Services are available at

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