All the R scripts needed to reproduce the figures in Fernandez-Guerrero et al. 2021.
This repository is a collaboration between @sofiasofia2208, @AleCaslbe and @lldelisle.
The pipeline.sh show you all the commands needed to reproduce the figures.
The scripts folder contains all the Rscripts.
The input folder contains the input tables.
The output folder contains intermediate results or tables.
The figure folder contains the images.
The additional_files folder contains tables as excel files.
To make the coverage plots in figure 2. We used pyGenomeTracks. The pgt.sh show you all the commands needed to reproduce the coverage plot. The inputs are in pgt_input and the outputs in output_pgt.