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MeRIPseqPipe

MeRIP-seq analysis pipeline

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker/singularity containers making installation trivial and results highly reproducible.  N6-methyladenosine (m6A) is the most prevalent modification in the mRNA of many eukaryotic species, including yeast, plants, flies, and mammals. In order to analyze m6A-seq data, we developed a user-friendly, integrated analysis pipeline called MeRIPseqPipe based on Nextflow. It integrated ten main functional modules including data preprocessing, quality control, read mapping, peak calling, peak merging, motif searching, peak annotation,differential methylation analysis, differential expression analysis, and data visualization. 

MeRIPseqPipe: Documentation

The MeRIPseqPipe documentation is split into the following files:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Dependencies

• Softwares
  • Fastqc
  • Fastp
  • RSeQC
  • MultiQC
  • STAR
  • BWA
  • TopHat
  • HISAT2
  • Bowtie2
  • samtools
  • MeTPeak
  • MATK
  • Meyer
  • MACS2
  • BEDtools
  • RobustRankAggreg
  • MeTDiff
  • QNB
  • htseq
  • deseq2
  • edgeR
  • cufflinks
  • Several R packages for downstream analysis.