update documentation with images

* [Peak calling](#peak-calling)

    * [SEACR](#seacr) - Peak calling for high signal-noise data

    * [Deeptools](#deeptools) - Analysis of peaks

    * [BEDTools](#bedtools) - merge peaks to create consensus peaks

* [Summary and quality control](#summary-and-quality-control)

    * [DESeq2](#deseq2) - PCA plot and differential peak analysis

    * [Python reporting](#python-reporting)

[Deeptools](https://github.com/deeptools/deepTools/) sub-tools computeMatrix and plotHeatmap are used to assess the distribution of fragments around genes and peaks.

### BEDtools

<details markdown="1">

<summary>Output files</summary>

* `seacr/`

    * `{group}.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across replicates within groups

    * `all_peaks.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across all samples

* `seacr/consensus_peaks`

    * `{group}.consensus.peaks.bed`: BED containing consensus peaks for each group

    * `all_peaks.consensus.peaks.bed`: BED containing consensus peaks across all samples

</details>

The merge function from [BEDtools](https://github.com/arq5x/bedtools2) is used to merge replicate peaks of the same experimental group to create a consensus peak set. This can then optionally be filtered for consensus peaks contributed to be a threshold number of replicates using `--replicate_threshold`. Additionally, the same workflow is run merging across all samples.

![Peak calling - group consensus peak plot](images/consensus_peaks.png)

![Peak calling - group consensus peak plot](images/all_consensus_peaks.png)

##  Summary and quality control

###  DESeq2