SpliceLauncher

SpliceLauncher detects, annotates, and quantifies alternative splice junctions from RNA sequencing (RNAseq) data to support analysis of alternative splicing relevant to molecular diagnostics.

Key Features:

• Detection and Annotation: Identifies alternative splice junctions in RNAseq datasets and annotates them using genomic information from GFF (version 3) files and FASTA genome sequences.
• Quantification: Quantifies the relative abundance of identified alternative splicing events.
• Configuration Management: Includes a pre-configured config.cfg that specifies paths to required software and data files and supports updates in INSTALL mode to incorporate user-defined genomic resources.
• Genome Indexing and Data Extraction: Extracts exon and transcript information from GFF and FASTA inputs, indexes the genome using STAR (Spliced Transcripts Alignment to a Reference), and generates a BED file of exon coordinates, an sjdb file of intron coordinates, and a text file detailing transcript structures.

Scientific Applications:

• Pathogenic Splice Variant Identification: Supports identification of pathogenic variants that affect splicing by detecting and quantifying splice junction alterations from RNAseq.
• Molecular Diagnostics and Disease Research: Provides high-resolution splice junction data for studies of splicing alterations in genetic disorders and clinical molecular diagnostics.

Methodology:

Users define paths to necessary genomic files which are processed to extract exon, intron, and transcript information. The genome is indexed using STAR (Spliced Transcripts Alignment to a Reference) and splice junctions are annotated based on the extracted data. Alternative splicing events are quantified and results are output to BED, sjdb, and transcript text files.