Peak Calling Pipeline

A Nextflow pipeline to perform peak calling of ChIP-seq, ATAC-seq or CUT&Tag sequencing data.

The pipeline was created to run on the ETH Euler cluster and it relies on the server's genome files. Thus, the pipeline needs to be adapted before running it in a different HPC cluster.

Pipeline steps

1. MACS callpeak
2. SEACR [Optional]

Required parameters

[Peak calling without control samples]

List of input files in BAM/BED/BedGraph format or other format required by the peak caller, e.g. '.bam' or '.bedgraph'.

--input /cluster/work/nme/data/josousa/project/*.bam

or

[Peak calling with control samples]

A CSV file with the names of the treatment and control files in BAM/BED/BedGraph format or other format required by the peak caller, e.g. 'design.csv'.

--input /cluster/work/nme/data/josousa/project/design.csv

# The CSV file should have the following format:
treatment,control
/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep1.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep1.bam
/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep2.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep2.bam
/cluster/work/nme/data/josousa/project/SEQ01_H3K27me3_rep3.bam,/cluster/work/nme/data/josousa/project/SEQ01_input_rep3.bam

Output directory where the files will be saved.

--outdir /cluster/work/nme/data/josousa/project

Genomes

• Reference genome used during alignment. This will provide MACS with the appropriate genome size.

  --genome 'Mus_musculus_GRCm39'

  Available genomes:

      Mus_musculus_GRCm39 # Default
      Mus_musculus_GRCm38_p6
      Homo_sapiens_GRCh38_p14 
      Drosophila_melanogaster_BDGP6_46
      Caenorhabditis_elegans_WBcel235

Peak caller optional parameters

• Peak calling tool.

  --peak_caller 'macs' # Default
  
  # or
  
  --peak_caller 'seacr'

Extra arguments

• Option to add extra arguments to MACS callpeak. --macs_callpeak_args

• Option to add extra arguments to SEACR. --seacr_args

Acknowledgements

This pipeline was adapted from the Nextflow pipelines created by the Babraham Institute Bioinformatics Group and from the nf-core pipelines. We thank all the contributors for both projects. We also thank the Nextflow community and the nf-core community for all the help and support.