MeRIPseqPipe

MeRIPseqPipe performs end-to-end analysis of methylated RNA immunoprecipitation sequencing (MeRIP-seq) data to identify and functionally characterize RNA modifications such as N6-methyladenosine (m6A) through preprocessing, alignment, peak calling, and downstream analyses.

Key Features:

• Integrated Functional Analysis Modules: Provides modules for preprocessing, peak calling, and downstream functional analyses within a single pipeline framework.
• Nextflow and Docker Support: Implements the pipeline in Nextflow and packages components in Docker containers to standardize execution environments.
• Batch Processing Capability: Supports processing of multiple samples concurrently to accommodate high-throughput datasets.
• Structured Output Directory: Organizes outputs into a directory hierarchy that reflects analysis steps and the tools used for each step.
• Visualization Reports: Generates HTML reports containing tables and plots that summarize analysis results.

Scientific Applications:

• m6A modification studies: Enables identification and characterization of N6-methyladenosine (m6A) sites from MeRIP-seq data.
• Gene expression regulation: Supports investigation of how RNA modifications influence gene expression patterns.
• Cellular differentiation studies: Facilitates analysis of modification-associated changes during cellular differentiation.
• Disease mechanism and therapeutic target discovery: Assists in exploring roles of RNA modifications in disease mechanisms and potential therapeutic targets.

Methodology:

Implemented in Nextflow with Docker containers; computational steps explicitly include quality control, alignment, peak calling, and downstream functional analyses.