nf-core Methylseq

This workflow includes a runner for nf-core/methylseq (ver. 2.6.0).

The Workflow

nf-core/methylseq is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

The pipeline allows you to choose between running either Bismark or bwa-meth / MethylDackel. Choose between workflows by using --aligner bismark (default, uses bowtie2 for alignment), --aligner bismark_hisat or --aligner bwameth.

Parameters

All parameters are setup as nf-core documentation.

Example Usage

Running in Astrocyte interface

First, prepare a samplesheet with your input data that looks as follows, make sure to upload all relative files to the Astrocyte project:

sample,fastq_1,fastq_2,genome
SRR389222_sub1,SRR389222_sub1.fastq.gz,,
SRR389222_sub2,SRR389222_sub2.fastq.gz,,
SRR389222_sub2,SRR389222_sub3.fastq.gz,,

Most Astrocyte parameters are following nf-core parameters. Check the parameters as needed.

If input files mentioned by the design file are not public URL, please make sure to include them in input reads box.

If you have other input files (for parameters known_splices/bamqc_regions_file), please make sure to include them in input reads box as well.

Running in command line interface with Nextflow

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz
SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz
SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz
Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

nextflow run nf-core/methylseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Credits

These scripts were originally written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden.

• Main author:
  • Phil Ewels (@ewels)
• Maintainers:
  • Felix Krueger (@FelixKrueger)
  • Sateesh Peri (@Sateesh_Peri)
  • Edmund Miller (@EMiller88)
• Contributors:
  • Rickard Hammarén (@Hammarn)
  • Alexander Peltzer (@apeltzer)
  • Patrick Hüther (@phue)

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 the Slack #methylseq channel (you can join with this invite).

Citations

If you use nf-core/methylseq for your analysis, please cite it using the following doi: 10.5281/zenodo.1343417

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

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.