cuffcompare

cuffcompare compares assembled transcripts to reference annotations and tracks Cufflinks-generated transcripts across experiments to support transcript discovery and transcript-level quantification from RNA-Seq data.

Key Features:

• Transcript comparison: Compares newly assembled transcripts against reference annotations to classify known and novel transcript models.
• Tracking across experiments: Tracks Cufflinks-generated transcripts across different samples, conditions, or time points to enable cross-experiment comparison.
• Alternative transcription and splicing analysis: Accounts for alternative transcription start sites (TSS) and splice isoforms when classifying and comparing transcripts.
• Annotation-independence: Implements algorithms that do not rely on prior gene annotations, enabling discovery of previously unannotated transcripts.
• Integration with Cufflinks outputs: Operates on transcript assemblies produced by the Cufflinks suite for downstream classification and comparison.

Scientific Applications:

• Transcript discovery and annotation: Supports identification and classification of novel transcripts in RNA-Seq studies, as demonstrated by discovery of 3,724 previously unannotated transcripts in a mouse myoblast RNA-Seq dataset with over 430 million paired reads.
• Isoform and TSS dynamics: Detects shifts in dominant transcription start sites and splice isoform usage across time series experiments, including complete switches in dominance for hundreds of genes (e.g., 330 genes) and more subtle shifts in others (e.g., 1,304 genes).
• Comparative transcriptomics: Enables comparison of transcript structures and expression patterns across experimental conditions to investigate gene regulation and transcriptome complexity.

Methodology:

Classifies and compares assembled transcripts against reference annotations, tracks Cufflinks-generated transcripts across experiments, accounts for alternative TSS and splice isoforms, and uses algorithms that do not rely on prior gene annotations.