Differential RNA-seq pipeline

Differential RNA-seq pipeline performs differential gene expression analysis of RNA sequencing (RNA-seq) data, including paired-end reads and pooled samples from animal studies generated by high-throughput cDNA sequencing technologies, using TopHat and Cufflinks to assemble transcripts, quantify abundance, and detect differentially expressed genes and transcripts in eukaryotic samples.

Key Features:

• Integration with TopHat and Cufflinks: Uses TopHat for read alignment and splice variant and novel gene identification and Cufflinks for transcript assembly, abundance quantification, and differential expression analysis.
• Support for paired-end reads and pooled samples: Processes paired-end sequencing data and pooled samples from animal studies.
• Comparative expression analysis: Compares gene and transcript expression across two or more conditions.
• Transcriptome assembly and outputs: Produces transcriptome assemblies and lists of differentially expressed genes and transcripts with associated quantifications.
• Visualization with CummeRbund: Generates visual representations of expression and differential analysis results using CummeRbund.

Scientific Applications:

• Gene discovery and splice variant detection: Identification of novel genes and splice variants in eukaryotic organisms.
• Comparative studies of conditions: Analysis of expression differences across biological conditions to investigate regulatory mechanisms.
• Phenotype, disease, and treatment studies: Elucidation of molecular underpinnings of phenotypic changes, disease progression, or responses to treatments.
• High-throughput dataset analysis: Handling complex, high-throughput cDNA sequencing datasets for transcriptome-level comparisons.

Methodology:

Starts from raw sequencing reads, performs read alignment to a reference genome with TopHat, assembles transcripts and quantifies abundance with Cufflinks, conducts differential expression analysis to identify genes and transcripts with significant expression changes between conditions, and generates visualizations with CummeRbund.