nf-core clipseq

nf-core clipseq analyzes Crosslinking and Immunoprecipitation (CLIP) sequencing data to preprocess reads, perform quality control, map reads to reference genomes, deduplicate Unique Molecular Identifiers (UMIs), and call peaks to identify protein–RNA interaction sites.

Key Features:

• Quality Control (QC): Implements QC steps with visualizations of quality control metrics for CLIP sequencing data.
• Pre-mapping: Performs pre-processing of raw CLIP reads prior to genome mapping.
• Genome Mapping: Maps sequencing reads to reference genomes to localize protein–RNA interaction sites.
• UMI Deduplication: Applies Unique Molecular Identifier (UMI) deduplication to reduce PCR amplification bias.
• Multiple Peak-Calling Options: Integrates multiple peak-calling tools to identify crosslinking peaks from CLIP data.
• Workflow Framework (Nextflow): Uses the Nextflow workflow framework for reproducible and portable pipeline execution.

Scientific Applications:

• Protein–RNA interaction mapping: Identification and characterization of protein–RNA interaction sites from CLIP sequencing experiments.
• Support for CLIP protocols: Applicable to diverse CLIP-based experimental protocols for studying RNA-binding proteins.

Methodology:

Implemented in the Nextflow framework with workflow management, version control, continuous integration, and containerization.