tdayris / fair_macs2_calling

Snakemake workflow used to call peaks with Macs2

Do not use. Active dev.

Snakemake workflow used to call peaks with Macs2 and annotate them with Homer.

Usage

The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.

Results

A complete description of the results can be found here in workflow reports.

Material and Methods

The tools used in this pipeline are described here textually. Web-links are available below:

Index and genome sequences with fair_genome_indexer

See pipeline content at fair_genome_indexer

Raw-sequences QC with fair_fastqc_multiqc

See pipeline content at fair_fastqc_multiqc

Bowtie2 Mapping with fair_bowtie2_mapping

See pipeline content at fair_bowtie2_mapping

Peak Calling

Step	Wrapper
Coverage analysis	deeptools-bamcoverage
Peak-Calling	macs2-callpeak
Annotation	homer-annotatepeaks

┌─────────────────────────────────────────┐
│ Aligned reads (see fair_bowtie2_mapping)│
└───────────────┬─────────────────────────┘
                │                          
                │                          
┌───────────────▼──────────┐               
│ Bam coverage (deeptools) │               
└───────────────┬──────────┘               
                │                          
                │                          
┌───────────────▼──────┐                   
│ Peak-Calling (Macs2) │                   
└───────────────┬──────┘                   
                │                          
                │                          
┌───────────────▼─────────┐                
│ Peak-Annotaiton (homer) │                
└─────────────────────────┘                

Quality Controls

Step	Wrapper/Official documentation
MultiQC	multiqc-wrapper
Finger prints	deeptools-plotfingerprint
Plot Coverage	deeptools-plotcoverage
Plot Enrichment	deeptools-plotenrichment
Plot PCA	deeptools-plotpca

                 ┌────────────────────┐                          
                 │fair_bowtie2_mapping├─────────────────────────┐
                 └─┬─────────┬────────┘                         │
                   │         │                                  │
                   │         │                                  │
┌──────────────────▼─┐       │    ┌────────────────────────┐    │
│Peak-calling (macs2)├───────┼────┤Correlations (deeptools)◄────┤
└──────────────────┬─┘       │    └────────────────────────┘    │
                   │         │                                  │
                   │         │                                  │
┌──────────────────▼────┐    │    ┌──────────────────────┐      │
│Peak-annotaiton (homer)├────┼────┤Enrichment (deeptools)◄──────┤
└───────────────────────┘    │    └──────────────────────┘      │
                             │                                  │
                             │                                  │
┌────────────────────┐       │     ┌───────────────┐            │
│ fair_fastqc_multiqc├───────┼─────┤PCA (deeptools)◄────────────┘
└────────────────────┘       │     └───────────────┘             
                             │                                   
                             │                                   
                             │                                   
                             │                                   
                         ┌───▼──────┐                            
                         │          │                            
                         │ MultiQC  │                            
                         │          │                            
                         └──────────┘