CracTools

CracTools analyzes RNA-Seq and digital gene expression (DGE) datasets to detect transcriptomic features including chimeric transcripts, splice variants, SNPs, and novel transcriptional regions.

Key Features:

• Chimeric Transcript Detection: Identifies chimeric RNA molecules derived from complex transcriptional events.
• Alternative Splicing Identification: Detects splice variants from RNA-Seq datasets to characterize transcript diversity.
• SNP Detection: Performs single nucleotide polymorphism (SNP) calling from transcriptome sequencing data.
• Novel Transcriptional Region Discovery: Integrates RNA-Seq and DGE tag data to identify previously unannotated transcribed regions.
• Genome Annotation Mapping: Maps uniquely aligned tags to the human genome using Ensembl references and categorizes them into protein-coding, antisense, intronic, or intergenic regions.
• Tissue-Specific Transcript Identification: Selects candidate transcripts showing tissue-specific expression patterns.

Scientific Applications:

• Transcriptome Analysis: Supports investigation of transcript structure, alternative splicing, and RNA variation using RNA-Seq and DGE data.
• Gene Regulation Studies: Enables identification of novel transcriptional regions and tissue-specific transcripts.
• Functional Genomics: Facilitates exploration of transcript diversity, genetic variation, and RNA-based regulatory mechanisms.

Methodology:

CracTools maps digital gene expression tags to a reference genome to detect novel transcriptional regions, validates these regions using RNA-Seq reads, and integrates tiling array expression data and species-comparison analyses for transcriptome characterization.