SEQualyzer

SEQualyzer performs quality control and exploratory analysis of high-throughput RNA structural profiling data to assess and standardize data quality for RNA structure studies.

Key Features:

• Visualization: Provides visualization of structural profiling data for exploration and assessment of data quality and complex dataset patterns.
• Quality-control metrics: Computes protocol-agnostic quantitative metrics common to RNA structure profiling protocols and screens transcripts for sufficient data quality.
• Discordant replicate detection: Identifies replicates with discordant results within experiments to pinpoint inconsistent or problematic datasets.
• Implementation: Implemented in R.

Scientific Applications:

• RNA structure determination: Supports analysis of high-throughput sequencing-based structure profiling experiments for interpreting RNA folding patterns.
• Standardization across protocols: Provides protocol-agnostic quality-control features common to a wide range of RNA structure profiling protocols to enable standardization of data quality assessment.

Methodology:

Calculates quantitative metrics derived from RNA structure profiling experiments in a protocol-agnostic manner and applies these metrics to screen transcripts and identify discordant replicates.