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Updated: Mar 7, 2026
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
Published on: November 7, 2025
SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling
Krishna Choudhary1, Luyao Ruan1, Fei Deng1
1Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
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.
Contact:
saviran@ucdavis.edu
Supplementary Informantion:
Supplementary data are available at Bioinformatics online.
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