Code and dataset for the manuscript "Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits"

Structure of the archive

The data generated in the manuscript is available in the dataset_sx folders:

dataset_s1/ contains the .bed files for predicted promoters, enhancers and primed enhancers in each of the 4 rodents.
dataset_s2/ contains the .bed files for predicted orthologous promoters and enhancers in each of the 4 rodents, along with tables of normalized H3k27ac read densities.
dataset_s3/ contains the .bed files for up and down enhancers and promoters in the 4 rodents, as identified by phylogenetic modeling.
dataset_s4/ contains the .fasta and .bed files for de novo repeat annotations, as well as .bed for non-alignable enhancers and their association with repeats.

The code to reproduce the main analyses presented in the manuscript is provided in the code folder, including:

A snakemake pipeline in nmrdmr_pipeline/, which (i) predicts regulatory elements from histone mark peaks, (ii) identifies orthologous elements across the 4 species and (iii) computes normalized H3k27ac read densities for orthologous elements, from the .bam files.
R scripts in phylogenetic_modeling/, to reproduce simulations and tests for up/down shifts using the evemodel R package.
A snakemake pipeline in snakeGREAT/, to perform functional enrichment on up/down elements in mole-rats, using the GREAT approach.