Differential abundance analysis
ChIP-seq peak-calling and differential analysis pipeline.
Type: Nextflow
Creators: Philip Ewels, Espinosa-Carrasco J, Patel H, Wang C, Ewels P
Submitter: WorkflowHub Bot
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
andH3K27me3_metadata_CLL.csv
), based on the same validation ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
ChIP-Seq pipeline
Here we provide the tools to perform paired end or single read ChIP-Seq analysis including raw data quality control, read mapping, peak calling, differential binding analysis and functional annotation. As input files you may use either zipped fastq-files (.fastq.gz) or mapped read data (.bam files). In case of paired end reads, corresponding fastq files should be named using .R1.fastq.gz and .R2.fastq.gz suffixes.
Pipeline Workflow
All analysis steps are illustrated in ...