epitranscriptomics

Overview

Analysis of RNA modifications (m6A, m5C) from MeRIP-seq and direct RNA sequencing.

Tool type: mixed | Primary tools: exomePeak2, MACS3, m6Anet, Guitar

Skills

Skill	Description
merip-preprocessing	Align MeRIP-seq IP and input samples with QC
m6a-peak-calling	Call m6A peaks from MeRIP-seq data
m6a-differential	Identify differential m6A methylation between conditions
m6anet-analysis	Detect m6A from ONT direct RNA sequencing
modification-visualization	Create metagene plots and browser tracks

Example Prompts

• "Align my MeRIP-seq IP and input samples"
• "Call m6A peaks from my MeRIP-seq data"
• "Find differential m6A sites between treatment and control"
• "Detect m6A modifications from my Nanopore direct RNA data"
• "Create a metagene plot of m6A distribution around stop codons"

Requirements

# R packages
BiocManager::install(c('exomePeak2', 'Guitar', 'GenomicFeatures'))

# Python packages
pip install m6anet ont-fast5-api

# CLI tools
conda install -c bioconda star macs3 samtools

Related Skills

• chip-seq - Similar peak-calling concepts
• rna-quantification - RNA-seq alignment
• long-read-sequencing - Nanopore data processing