kingzhuky/meripseqpipe repository overview

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

⁠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 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 m6APipe based on Nextflow. It integrated ten main functional modules including preprocessing, QC, read mapping, peak calling, merging peaks, differential methylation analysis, differential expression analysis, motif search, annotation, and data visualization.

⁠Quick Start

i. Install nextflow⁠

ii. Install one of docker⁠, singularity⁠ 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>

iv. Start running your own analysis!

nextflow run path/to/meripseqpipe -profile <docker/singularity/conda>  --designfile 'designfile.csv' --comparefile 'comparefile.txt'

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

⁠Documentation

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

⁠Credits

nf-core/meripseqpipe was originally written by Kaiyu Zhu, Yu Sun.

⁠Contributions and Support

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).

⁠Citation

You can cite the nf-core publication as follows: