QuasR

QuasR quantifies and analyzes short-read RNA-seq data to detect splice junctions, quantify genomic regions, and enable alternative splicing studies.

Key Features:

• End-to-End Workflow: Provides a workflow from raw sequence reads through alignment creation, quality-control plotting, and quantification of genomic regions of interest.
• High Sensitivity and Specificity: Detects splice junctions with high sensitivity and specificity.
• Novel Splice Junction Detection: Identifies novel splice junctions without relying on pre-existing gene structure annotations.
• Long Read Handling: Processes long reads ranging from 50-100 nucleotides and utilizes paired-read information to enhance mapping accuracy.
• Reliability Indicators: Outputs parameters that indicate the reliability of predicted splice junctions to aid filtration of false positives.

Scientific Applications:

• Alternative Splicing Analysis: Enables detection and quantification of alternative splicing events across different cell types using RNA-seq data.
• Human Brain Tissue Analysis: Has been applied to 23 million paired 50-nt reads from human brain tissue, supporting reliable detection of splice junctions except at very low expression levels.
• Benchmarking: Reported to achieve 12% higher sensitivity than existing methods without compromising specificity.

Methodology:

Employs the SpliceMap algorithm to detect splice junctions from RNA-seq without depending on existing gene annotations, handling 50-100 nucleotide reads and exploiting paired-read information to improve mapping accuracy.