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



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



saviran@ucdavis.edu



Supplementary data are available at Bioinformatics online.
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
Krishna
K
Choudhary
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
Luyao
L
Ruan
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
Fei
F
Deng
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
Nathan
N
Shih
Department of Biomedical Engineering and Genome Center, University of California at Davis, Davis, CA, USA.
Sharon
S
Aviran
D059014:High-Throughput Nucleotide Sequencing / Q000379:methods* / Q000592:standards; D011786:Quality Control; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards; D012984:Software