rnaSeqMap

rnaSeqMap analyzes RNA sequencing (RNA-seq) data to compute coverage profiles, detect novel transcriptional regions, and perform nucleotide-level significance and splicing analyses for transcriptomics research.

Key Features:

• Coverage Analysis: Computes detailed coverage profiles across multiple samples to quantify RNA expression depth.
• Novel Transcription Region Discovery: Detects novel or non-annotated transcripts using gene annotations or unsupervised discovery across genomic regions.
• Data Management Flexibility: Supports MySQL database back-ends and standard BAM files for storage and access of sequencing data.
• Scalability and Efficiency: Processing scales linearly with the number of genomic loci and samples and does not require specialized hardware.
• Coverage Operations: Performs comprehensive coverage operations to characterize expression profiles.
• Irreducible Regions Identification: Identifies irreducible high-expression regions to localize significant transcriptional activity.
• Significance Search and Splicing Analyses: Performs significance testing and splicing analyses at nucleotide-level granularity.

Scientific Applications:

• Expression Profiling: Quantify gene and transcript expression levels from RNA-seq coverage.
• Transcript Discovery: Discover novel transcriptional regions and unannotated transcripts.
• Alternative Splicing Analysis: Analyze splicing patterns and alternative isoforms at nucleotide resolution.
• Gene Regulation Studies: Investigate regulatory changes reflected in coverage and splicing patterns.
• Large-Scale Transcriptomics: Support large-scale transcriptome exploration across many samples and loci.

Methodology:

Computes per-sample coverage profiles; identifies novel transcriptional regions via annotation-guided or unsupervised methods; performs coverage operations, irreducible-region detection, significance searches, and nucleotide-level splicing analyses; and operates on MySQL and BAM back-ends with processing scaling linearly with loci and samples.