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 │ │ │ └──────────┘