RNA-seq Pipeline

RNA-seq Pipeline processes RNA sequencing (RNA-seq) data from next-generation sequencing to align reads, generate signal tracks, and quantify genes and isoforms to support clinical genetic diagnosis and detection of splicing-related regulatory events.

Key Features:

• Alignment of Reads: Aligns RNA-seq reads to reference genomes to provide accurate mapping for downstream analyses.
• Signal Track Generation: Generates signal tracks representing expression levels across genomic regions for quantitative and visual interpretation.
• Quantification of Genes and Isoforms: Quantifies gene expression and transcript isoforms to capture differential splicing and variant expression.
• Variant Identification and Annotation: Identifies, annotates, and classifies sequence variants from RNA-seq data.
• Next-generation Sequencing Support: Processes RNA-seq datasets produced by next-generation sequencing technologies.
• Provenance: Implementation originates from the ENCODE-DCC RNA-sequencing pipeline.

Scientific Applications:

• Clinical Genetic Diagnosis: Aids identification, annotation, and classification of sequence variants in clinical genetic diagnosis and enhances detection of splicing events and variants, potentially increasing diagnostic rates by 10–35%.
• Splicing and Regulatory Event Analysis: Links differential splicing and other regulatory events to disease phenotypes.
• Transcriptome Profiling: Profiles transcriptome variation across tissue types, cellular conditions, and environmental factors.

Methodology:

The pipeline employs advanced bioinformatics processing algorithms and computational and statistical tools, may require customization for specific diseases, and emphasizes best practices in RNA-seq analysis.