Functional enrichment for mole-rat cis-regulatory elements

This folder contains an implementation of some of the GREAT functional enrichment tests for cis-regulatory regions, that we applied to mole rats regulatory shifts. Note that the code in intended for repoducibility only, and that more robust packages have re-implemented GREAT since (see rGREAT).

Setting up and activating the environment

mamba env create -f env.yaml

conda activate snake_great

Running

The following command runs enrichment tests on heart enhancers UP in the ancestral mole-rat branch, using the Damaraland mole-rat (Fdam) genome as background. The pipeline automatically finds the corresponding .bed files in the dataset_s2 and dataset_s3 folders. Results are stored in a new GO_GREAT_RESULTS_ folder.

snakemake -s great_hgla_fdam.smk --cores 4 --config sp=Fdam t=Heart r=Enhancers b=ancestral_MR_branch s=UP

The following command runs enrichment tests on heart enhancers DOWN in the naked mole-rat branch, using the naked mole-rat (Hgla) genome as background:

snakemake -s great_hgla_fdam.smk --cores 4 --config sp=Hgla t=Heart r=Enhancers b=Hgla_branch s=DOWN

The following command is similar to the previous one, but filters out heart hgla DOWN enhancers by removing heart enhancers also found as DOWN in the ancestral mole-rat branch (we used this redundancy filter to compare enrichments across branches).

snakemake -s great_hgla_fdam.smk --cores 4 --config sp=Hgla t=Heart r=Enhancers b=Hgla_branch s=DOWN reduce=y