RNASeqBrowser

RNASeqBrowser: RNA-seq Data Visualization and Analysis Platform

RNASeqBrowser visualizes and analyzes RNA-seq data by dynamically generating read coverage, SNP, InDel, and raw read tracks from BAM files, supporting strand-specific transcript interpretation and detection of transcriptomic features.

Key Features:

• Platform Integration: Incorporates functionalities from the UCSC Genome Browser and IGV to enable analysis of next-generation sequencing (NGS) RNA-seq datasets.
• Comprehensive Data Display: Simultaneously displays read coverage, single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and raw read tracks dynamically generated from BAM files.
• Strand-Specific Visualization: Differentiates positive and negative strand transcripts to support strand-specific RNA-seq analysis.
• Novel Exon/Intron Identification: Connects paired-end reads to detect novel exon–intron boundaries, alternative splicing events, and chimeric transcripts.
• RNA Secondary Structure Prediction: Generates RNA secondary structure models to support identification of non-coding RNAs, including microRNAs (miRNAs).
• Differential Expression Visualization: Overlays NGS wiggle data to visualize differential expression patterns across datasets.
• Duplicate Read Collapsing: Collapses identical reads to optimize computational performance and visualization efficiency.

Scientific Applications:

• Transcriptome Analysis: Supports gene expression analysis, transcriptome profiling, genetic variant identification, and investigation of alternative splicing and regulatory RNA elements in molecular and clinical research.

Methodology:

Processes RNA-seq alignment data from BAM files to dynamically construct coverage plots, variant tracks, and read alignments; integrates paired-end read connectivity for exon–intron boundary detection; applies RNA secondary structure prediction algorithms for non-coding RNA analysis; and overlays wiggle-based NGS signal tracks for comparative expression assessment.