TEtranscripts

TEtranscripts performs differential expression analysis of RNA-seq data by apportioning ambiguously mapped short sequencing reads between genes and transposable elements to quantify TE and gene expression.

Key Features:

• Inclusion of Transposable Elements: Assigns ambiguously mapped reads to both genes and transposable elements to include TEs in expression measurements.
• Differential Expression Testing: Performs differential expression testing that incorporates both gene-associated and TE-associated reads.
• Statistical Analysis: Provides statistical analysis tailored to assess expression levels of transposable elements alongside traditional genes.
• Improved Recovery of TE Transcripts: Demonstrates improved recovery of TE transcripts relative to other published methods, validated using synthetic data simulations and real datasets verified by qPCR and NanoString.
• Ambiguous Read Apportionment: Employs a novel method to apportion ambiguously mapped reads between genomic features.
• TE GTF Annotation: Uses associated GTF files specifically designed for transposable element annotation to guide read assignment.

Scientific Applications:

• Genomic Studies: Quantifies the contribution of transposable elements to transcriptomic and genomic read pools for studies of genome architecture and evolution.
• Gene Regulation Research: Enables investigation of how transposable elements influence gene expression patterns and regulatory networks.
• Comparative Genomics: Allows analysis of TE activity and expression differences across species or experimental conditions to infer evolutionary processes.

Methodology:

Apportions ambiguously mapped short RNA-seq reads between genes and transposable elements using a novel allocation method and leverages TE-specific GTF annotation files to guide read assignment.