GRAPE 2.0

GRAPE 2.0 performs end-to-end RNA-Seq data processing to enable quality control, read alignment, expression quantification, exon inclusion analysis, and novel transcript identification for transcriptomic research.

Key Features:

• Compatibility with Various Data Formats: Supports raw sequencing reads from NGS platforms in FASTA and FASTQ formats and accepts prealigned reads in SAM and BAM formats.
• Modular Design for Customization: Provides a modular architecture that allows integration of additional mapping and quantification tools that follow common data interchange formats.
• Comprehensive Workflow: Implements quality control of reads, alignment to a specified reference genome for non-prealigned data, gene and transcript expression estimation, exon inclusion level calculation, and novel transcript identification.
• Scalability and Performance: Can run on a single computer or be executed in parallel across a computer cluster to accommodate large datasets.

Scientific Applications:

• Gene Expression Profiling: Quantifies gene and transcript expression levels across samples or conditions.
• Alternative Splicing Studies: Calculates exon inclusion levels to analyze splicing variants and their regulation.
• Discovery of Novel Transcripts: Identifies previously unannotated transcripts to expand transcriptome annotation.

Methodology:

The pipeline performs quality control on raw FASTA/FASTQ reads or prealigned SAM/BAM files, aligns reads to a reference genome when required, quantifies gene and transcript expression, computes exon inclusion levels, and detects novel transcripts.