SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data

• DOI: 10.1093/bioinformatics/btw627
• Publication Date: 2016-09-29T19:06:19Z
• Authors: Krishna Choudhary; Luyao Ruan; Fei Deng; Nathan Shih; Sharon Aviran
• Keywords: Quality Control; 0301 basic medicine; Bioinformatics; Sequence Analysis, RNA; Human Genome; Bioinformatics and Computational Biology; Mathematical sciences; High-Throughput Nucleotide Sequencing; Biological Sciences; Mathematical Sciences; Biological sciences; 03 medical and health sciences; Information and Computing Sciences; Genetics; Information and computing sciences; RNA; Sequence Analysis; Software

Abstract

Summary To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approaches continues to emerge, a universal framework is needed to quantitatively ensure consistent and high-quality data. We present SEQualyzer, a visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure profiling experiments. Our methods rely on features common to a wide range of protocols and can serve as standards for quality control and analyses.

Availability and Implementation SEQualyzer is written in R, is platform-independent, and is freely available at http://bme.ucdavis.edu/aviranlab/SEQualyzer.

Supplementary information Supplementary data are available at Bioinformatics online.