Grape

Grape analyzes RNA sequencing (RNA-Seq) data from Next Generation Sequencing (NGS) platforms to perform alignment, gene and transcript expression quantification, exon inclusion estimation, and novel transcript discovery for transcriptome characterization.

Key Features:

• Versatile Input Support: Accepts raw reads in FASTA or FASTQ formats and prealigned reads in SAM/BAM format from various NGS platforms.
• Modular Pipeline Design: Performs quality control and, for non-prealigned reads, aligns to a reference genome using integrated mapping tools and supports integration of alternative mapping and quantification tools that use common data interchange formats.
• Comprehensive Analysis Capabilities: Estimates gene and transcript expression levels, calculates exon inclusion levels, and identifies novel transcripts.
• Scalability: Operates on single computers and parallel computing clusters to accommodate large-scale studies.
• Required Inputs: Accepts raw sequencing reads or prealigned reads, a reference genome, and corresponding gene and transcript annotations.

Scientific Applications:

• Differential expression analysis: Enables gene- and transcript-level quantification for differential expression studies.
• Alternative splicing studies: Provides exon inclusion level calculations to study alternative splicing events.
• Novel transcript discovery: Detects previously unannotated transcripts within RNA-Seq datasets.

Methodology:

Computational steps explicitly include quality control of raw reads; mapping reads to a reference genome for non-prealigned data using integrated mapping tools; quantification of gene and transcript expression using integrated tools; calculation of exon inclusion levels; and detection of novel transcripts.