This GitHub page contains all scripts that were used to create the figures for the LAD borders manuscript with AID-mediated depletion of CTCF and proteins involved in (loop) extrusion, by Tom van Schaik et al., 2021/2022 (https://doi.org/10.1101/2021.09.13.460079).
DamID processing was performed with a custom snakemake pipeline (damid_processing/bin/snakemake/damid.snake), using a configuration file with information on the samples (damid_processing/bin/snakemake/config.yaml). The other data was processed as described in the accompanying manuscript.
Except the initial data processing, all data analysis was performed in R using R-markdown scripts. These scripts are also included here and provide introductions and conclusions of the described analyses. It is important to highlight that these scripts were not filtered to only include the figure panels that were used in the manuscript. This should provide a more transparant overview of our data analysis.