eXpress

eXpress quantifies transcript and other target-sequence abundances from high-throughput sequencing reads (including RNA-Seq) by correcting for non-uniform cDNA fragment distributions.

Key Features:

• Likelihood-Based Correction: Employs a likelihood-based approach to correct biases introduced during RNA-Seq library preparation, accounting for non-uniform cDNA fragment distributions across transcripts.
• Ambiguous Mapping Resolution: Resolves ambiguous read mappings by integrating them into the likelihood-based correction framework.
• Enhanced Expression Estimates: Produces improved expression level estimates that show better correlation with independent qRT-PCR measurements.
• Improved Replicability: Mitigates biases that cause variability, enhancing replicability across libraries and sequencing technologies.

Scientific Applications:

• Transcript-Level RNA-Seq Quantification: Provides accurate transcript abundance estimates for gene expression studies.
• Allele-Specific/Haplotype Expression Analysis: Facilitates analysis of allele-specific or haplotype-resolved expression from RNA-Seq data.
• Transcription Factor Binding Quantification in ChIP-Seq: Can be applied to quantify transcription factor binding events from ChIP-Seq data.
• Metagenomic Data Analysis: Supports quantification of target sequences in metagenomic datasets to study microbial community composition and function.

Methodology:

Resolves ambiguous mappings and applies a likelihood-based correction for non-uniform cDNA fragment distributions to adjust abundance estimates.