TRAPLINE

TRAPLINE processes RNA sequencing (RNAseq) data to standardize and automate analysis, evaluation, and prediction for downstream applications including differential expression, protein-protein interaction prediction, splice variant and promoter-enriched site detection, miRNA-target prediction, and generation of files for SNP calling.

Key Features:

• Platform Compatibility: Optimized for Illumina FASTQ reads and also supports SOLiD and Solexa sequencing platforms for NGS RNAseq data.
• Integrated Workflow: Integrates data analysis, evaluation, and annotation methods into a cohesive automated workflow for transcriptome processing.
• Differential Expression Analysis: Identifies differentially expressed genes from comparative transcriptomics analyses.
• Protein-Protein Interaction Prediction: Predicts protein-protein interactions to provide insights into cellular functions and pathways.
• Splice Variant and Promoter-Enriched Site Detection: Detects alternative splicing variants and promoter-enriched sites relevant to gene regulation.
• miRNA-Target Predictions: Predicts miRNA-target interactions to support studies of post-transcriptional regulation.
• SNP Calling Outputs: Generates files suitable for single nucleotide polymorphism (SNP) calling and downstream variation analyses.
• Reproducibility: Implemented within the Galaxy biomedical research platform to support transparent and reproducible workflows.

Scientific Applications:

• Comparative Transcriptomics: Supports identification of differential gene expression and transcriptome changes across conditions using RNAseq data.
• Transcriptome Characterization: Enables characterization of complex transcriptomes, exemplified by analysis of stem cell-derived antibiotic-selected cardiac bodies (aCaBs).

Methodology:

Implemented as a Galaxy workflow that processes Illumina FASTQ, SOLiD, and Solexa RNAseq reads and integrates data analysis, evaluation, and annotation methods to produce outputs for differential expression, protein-protein interaction prediction, splice variant and promoter-enriched site detection, miRNA-target prediction, and files for SNP calling.