CoCo

CoCo reassigns RNA-seq reads to account for nested genes and multi-mapped reads, improving transcript quantification in higher eukaryotic transcriptomes.

Key Features:

• Nested-gene-aware read assignment: Implements a read assignment pipeline that accounts for nested genes and overlapping annotations.
• Modified annotation: Uses a modified annotation file specifically designed to highlight nested genes.
• Multi-mapped read allocation: Proportionally allocates multi-mapped reads among repeated sequences.
• Read recovery: Recovers over 15% of previously discarded aligned RNA-seq reads.
• Impact on quantification: Alters abundance estimates for both coding and non-coding RNAs by redistributing reads.
• Validation: Validation reported using PCR and bedgraph comparisons.

Scientific Applications:

• Transcript quantification: Improves quantification accuracy in RNA-seq experiments from higher eukaryotic transcriptomes with nested and repetitive genes.
• Gene expression studies: Enhances reliability of coding and non-coding RNA abundance estimates for gene expression analyses.
• Next-generation sequencing analyses: Applies to RNA-seq datasets generated by next-generation sequencing technologies where multi-mapped reads and nested genes affect read assignment.

Methodology:

A read assignment pipeline uses a modified annotation file to mark nested genes and proportionally allocates multi-mapped reads among repeated sequences.