Pipeline for identification of CEs/CNEs for the mm10 mouse genome, to be used for population genetics. Using phastCons and UCSC alignments, but masking mouse and rat sequences to avoid ascertainment bias from mouse/rat divergence.
File of CEs (ens_mm10_CEs.bed) and CNEs (ens_mm10_CNEs.bed) can be produced by running: bash pipeline.sh
Requirements:
PHAST v1.4 - https://github.com/CshlSiepelLab/phast
bedtools v2.26.0 - https://github.com/arq5x/bedtools2
BioPerl modules AlignIO and SimpleAlign