Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.

A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:

• Peak calling
• Consensus peak count table generation
• Detection of super-enhancer regions
• Differential binding analysis

On the respective GitHub folder are available:

• The CWL wrappers for the workflow
• A pre-configured YAML template, based on validation analysis of publicly available HTS data
• Tables of metadata (EZH2_metadata_CLL.csv and H3K27me3_metadata_CLL.csv), based on the same validation ...

This workflow is designed to analyze to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies. (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant ...