ASJA

ASJA identifies and characterizes linear, back-splice, and fusion splice junctions from high-throughput RNA sequencing (RNA-seq) data to enable detection and quantification of alternative splicing events.

Key Features:

• Comprehensive Junction Identification: Identifies a wide array of splice junction types including linear, back-splice, and fusion junctions from RNA-seq data.
• Integration with STAR and StringTie: Processes alignments and chimeric alignments generated by the STAR aligner and assembled transcripts produced by StringTie.
• Unique Positioning and Expression Quantification: Determines the unique genomic position for each splice junction and reports normalized expression levels.
• Annotation and Integrative Analysis: Annotates splice junctions with relevant genomic information and supports integrative analyses for additional filtering and validation.
• Novel Junction Discovery: Detects splice junctions not present in reference databases to identify novel splicing events.

Scientific Applications:

• Gene Expression Studies: Quantifies splice junctions to analyze gene expression patterns and their variation across conditions or disease states.
• Splicing Regulation Research: Supports investigation of regulatory mechanisms underlying alternative splicing and their effects on protein diversity.
• Novel Transcript Discovery: Enables discovery of novel transcripts and splice variants to improve genome annotation and transcriptome characterization.

Methodology:

Processes STAR aligner outputs (including chimeric alignments) and StringTie assembled transcripts; applies algorithms to detect linear, back-splice, and fusion junctions; annotates junctions with genomic information; determines unique junction positions and computes normalized expression levels.