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QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments.
Stephen W Hartley1, James C Mullikin2
1Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA. stephen.hartley@nih.gov.
BMC Bioinformatics
|July 19, 2015
Summary
The Quality of RNA-Seq Toolset (QoRTs) enhances RNA sequencing analysis by providing comprehensive quality control metrics. This toolset identifies potential biases and errors, ensuring reliable transcript expression and regulation data.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- High-throughput next-generation RNA sequencing is a powerful tool for analyzing gene expression.
- Ensuring data quality is crucial to avoid false associations and flawed results in RNA sequencing studies.
Purpose of the Study:
- To introduce the Quality of RNA-Seq Toolset (QoRTs) for comprehensive quality control and data processing of RNA sequencing data.
Main Methods:
- Development of a multifunction toolset named QoRTs.
- Implementation of quality control and data processing functionalities for RNA sequencing data.
Main Results:
- QoRTs provides a wide array of quality control metrics.
- The toolset enables cross-comparisons of replicates to identify outliers and systematic issues.
- QoRTs generates coverage counts for genes, exons, and splice-junctions, along with browser tracks.
Conclusions:
- QoRTs enhances the reliability of RNA sequencing analyses by detecting potential biases and errors.
- The toolset streamlines data processing and quality control into a single, efficient pipeline.
- QoRTs is available online with source code and documentation.
