RAP

RAP performs comprehensive RNA-Seq data analysis to identify and quantify genes and transcripts, detect alternative splicing and chimeric transcripts, analyze splicing junctions and constitutive and alternative polyadenylation sites, and call differential expression.

Key Features:

• Modular Analysis Workflow: Implements a modular workflow that integrates state-of-the-art bioinformatics tools and custom-developed scripts for flexible transcriptome analysis.
• Quality Control: Performs read- and sample-level quality checks using FastQC and NGS QC Toolkit.
• Gene and Transcript Identification & Quantification: Uses Tophat, Cufflinks, and HTSeq to align reads and quantify expressed genes and transcripts.
• Alternative Splicing Detection: Detects alternative splicing events using SpliceTrap.
• Chimeric Transcripts Identification: Identifies chimeric transcripts and potential fusion events with ChimeraScan.
• Splicing Junctions and Polyadenylation Sites Analysis: Applies custom analysis modules to identify splicing junctions and both constitutive and alternative polyadenylation sites.
• Differential Expression Analysis: Calls differential expression and tests for changes in splicing and polyadenylation usage using Cuffdiff2 and DESeq.

Scientific Applications:

• Gene and Transcript Quantification: Identification and quantification of expressed genes and transcripts from RNA-Seq data.
• Alternative Splicing and Polyadenylation Analysis: Analysis of alternative splicing events and constitutive and alternative polyadenylation site usage.
• Fusion Gene and Trans-Splicing Detection: Detection of fusion genes and trans-splicing occurrences via chimeric transcript identification.
• Post-Transcriptional Modification Examination: Examination of splicing junctions and polyadenylation as aspects of post-transcriptional regulation.

Methodology:

Implements a modular pipeline integrating FastQC and NGS QC Toolkit for quality control; Tophat, Cufflinks, and HTSeq for alignment and quantification; SpliceTrap for alternative splicing detection; ChimeraScan for chimeric transcript detection; custom modules for splicing junction and polyadenylation site identification; and Cuffdiff2 and DESeq for differential expression analysis.