UTAP

UTAP performs end-to-end processing of RNA-Seq and bulk MARS-Seq cDNA sequencing data to generate transcriptome-level results and identify sets of differentially expressed genes from high-throughput instruments such as Illumina Next-Seq.

Key Features:

• Comprehensive workflow: Executes an end-to-end analysis starting from cDNA sequences produced by RNA-Seq and bulk MARS-Seq library preparations to downstream transcriptome results.
• Differential expression analysis: Produces sets of differentially expressed genes from processed sequencing data.
• Support for library types: Processes data derived from RNA-Seq and bulk MARS-Seq library preparation methods.
• Scalability: Handles large high-throughput sequencing datasets generated by instruments such as Illumina Next-Seq.
• Structured output: Organizes results into structured folders and generates plots, tables, and links summarizing analysis outcomes.

Scientific Applications:

• Transcriptome characterization: Characterizes transcriptomes from RNA-Seq and MARS-Seq datasets.
• Differential expression studies: Detects gene expression differences across cell types, genotypes, and experimental conditions.
• Multi-library analyses: Enables analysis of datasets produced by different library preparation methods for comparative genomics studies.

Methodology:

Integrates state-of-the-art bioinformatics tools and automates the analysis workflow, tailoring processing steps according to each RNA-Seq library preparation type.