MeRIP-seq analysis pipeline arranged multiple alignment tools, peakCalling tools, Merge Peaks' methods and methylation analysis methods..

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 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. 

i. Install nextflow

ii. Install one of docker or conda

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run path/to/meripseqpipe -profile test,<docker/singularity/conda>

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or conda and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run path/to/meripseqpipe -profile <docker/singularity/conda> --designfile 'designfile.tsv' --comparefile 'comparefile.txt'  --fasta path/to/genome_fasta.fa --gtf path/to/genome_annotation.gtf

See usage docs for all of the available options when running the pipeline.

The nf-core/meripseqpipe pipeline comes with documentation about the pipeline, found in the docs/ directory:

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

MeRIPseqPipe was originally written by Kaiyu Zhu, Yu Sun, Xiaoqiong Bao.

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on Slack (you can join with this invite).

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
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