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Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive.

Matthew N Bernstein1, Ariella Gladstein2, Khun Zaw Latt3

  • 1Morgridge Institute for Research, Madison, Wisconsin, 53715, USA.

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|September 3, 2020
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Summary
This summary is machine-generated.

New tools leverage standardized metadata from MetaSRA to enable secondary analysis of human RNA-sequencing (RNA-seq) data in the Sequence Read Archive (SRA). These tools facilitate the identification of case-control and time-series sample sets for research.

Keywords:
HackathonJupyterMetaSRAMetadataOntologyRNA-seqSequence Read Archive

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Science

Background:

  • The Sequence Read Archive (SRA) is a vast repository for next-generation sequencing data.
  • Metadata heterogeneity and quality issues in the SRA hinder data reuse and re-analysis.
  • The MetaSRA project standardized SRA metadata using biomedical ontologies.

Purpose of the Study:

  • To develop tools for building structured datasets from SRA data.
  • To facilitate secondary analyses of human RNA-sequencing (RNA-seq) data.
  • To enable efficient retrieval of specific sample sets for research.

Main Methods:

  • Developed two Jupyter notebook-based tools: Case-Control Finder and Series Finder.
  • Utilized the standardized MetaSRA database for data annotation.
  • Focused on human RNA-seq data within the SRA.

Main Results:

  • The Case-Control Finder identifies matched case and control samples for specific conditions.
  • The Series Finder retrieves ordered sample sets for analyzing changes over numerical properties (e.g., time).
  • These tools streamline the process of accessing and utilizing SRA data for research.

Conclusions:

  • The developed tools enhance the usability of the SRA for human RNA-seq data analysis.
  • Standardized metadata is crucial for unlocking the full potential of large public sequencing repositories.
  • These tools support hypothesis-driven research by facilitating structured data retrieval.