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mouse_mm10_conserved_elements

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

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code to identify conserved elements for mm10 mouse genome

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  • Perl 69.9%
  • Shell 30.1%