Input files for this analysis can be obtained from zenodo.
The Snakefile
in this directory contains all rules used to evaluate the HiC
enrichment for longrange
(TAD + HiC) and trans
meQTL pairs.
Can be executed using snakemake, e.g.:
snakemake --profiles profiles/default all_hic
The report.Rmd
can be generated after running the snakemake workflow.
The markdown was originally in a separate 'master-report' for the full meQTL
project, and the parts relevant for the HiC enrichment have been extracted.
Generate the report e.g. using:
R -e "rmarkdown::render('report.Rmd')"