MeRIP-PF

MeRIP-PF identifies high-resolution N(6)-methyladenosine (m(6)A) peaks from Methylation of RNA Immunoprecipitation sequencing (MeRIP-Seq) data by comparing read distributions between experimental samples and controls to map and quantify m(6)A-modified regions.

Key Features:

• High-resolution peak finding: Detects m(6)A-modified regions in MeRIP-Seq data through comparison of read distributions between experimental samples and controls.
• Statistical validation (P-values): Calculates statistical P-values for each identified m(6)A region to quantify significance relative to control data.
• False Discovery Rate (FDR): Implements FDR calculations as a cutoff criterion to control false positives in peak identification.
• Gene annotation: Provides gene-level annotation for detected m(6)A signals or peaks to support downstream interpretation.
• Output formats: Produces results in XLS format and as graphical representations for analysis and visualization.

Scientific Applications:

• Epitranscriptomic mapping: Mapping the distribution of m(6)A across transcripts to study epitranscriptomic landscapes.
• Regulation of gene expression: Investigating how m(6)A modifications influence gene expression regulation and RNA stability.
• Comparative MeRIP-Seq analysis: Comparing experimental and control samples to identify differential m(6)A-modified regions.

Methodology:

Implemented in Perl; processes MeRIP-Seq data by comparing read distributions between experimental samples and controls, applies statistical methods to compute P-values and FDR for identified m(6)A regions, and annotates significant peaks.