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GO.step80.create_bigBed_files
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GO.step80.create_bigBed_files
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# ################################################################################################################################################################################################################
# GO.step80.create_bigBed_files
#
# CC-BY Lee Edsall
# email: le49@duke.edu
# Twitter: @LeeEdsall
#
# This script was used to analyze data for Edsall et al. 2019 which compared DNase-seq data from 5 primates (human, chimpanzee, gorilla, orangutan, macaque)
# ################################################################################################################################################################################################################
# --------------------------------------------------------------------------------------------------------------------------------------------------
# DHS sites
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.passed_coverage_filter.zero_filtered.bed all_DHS_sites.bb
source GO.create_bigBed_file human_DHS_sites.bed human_DHS_sites.bb
source GO.create_bigBed_file chimp_DHS_sites.bed chimp_DHS_sites.bb
source GO.create_bigBed_file gorilla_DHS_sites.bed gorilla_DHS_sites.bb
source GO.create_bigBed_file orangutan_DHS_sites.bed orangutan_DHS_sites.bb
source GO.create_bigBed_file macaque_DHS_sites.bed macaque_DHS_sites.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# All differential; all non-significant
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.differential_sites.locations.bed DHS_sites.differential.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.not_significant_sites.locations.bed DHS_sites.not_significantly_differential.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.Gsss.locations.bed DHS_sites.Gsss.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.Lsss.locations.bed DHS_sites.Lsss.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Chimp
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sGss.locations.bed DHS_sites.sGss.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sLss.locations.bed DHS_sites.sLss.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Gorilla
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.ssGs.locations.bed DHS_sites.ssGs.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.ssLs.locations.bed DHS_sites.ssLs.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sssG.locations.bed DHS_sites.sssG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sssL.locations.bed DHS_sites.sssL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# HCGO
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GGGG.locations.bed DHS_sites.GGGG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LLLL.locations.bed DHS_sites.LLLL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and chimp
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GGss.locations.bed DHS_sites.GGss.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LLss.locations.bed DHS_sites.LLss.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and gorilla
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GsGs.locations.bed DHS_sites.GsGs.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LsLs.locations.bed DHS_sites.LsLs.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GssG.locations.bed DHS_sites.GssG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LssL.locations.bed DHS_sites.LssL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Chimp and gorilla
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sGGs.locations.bed DHS_sites.sGGs.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sLLs.locations.bed DHS_sites.sLLs.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Chimp and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sGsG.locations.bed DHS_sites.sGsG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sLsL.locations.bed DHS_sites.sLsL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Gorilla and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.ssGG.locations.bed DHS_sites.ssGG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.ssLL.locations.bed DHS_sites.ssLL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and chimp and gorilla
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GGGs.locations.bed DHS_sites.GGGs.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LLLs.locations.bed DHS_sites.LLLs.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and chimp and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GGsG.locations.bed DHS_sites.GGsG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LLsL.locations.bed DHS_sites.LLsL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Human and gorilla and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.GsGG.locations.bed DHS_sites.GsGG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.LsLL.locations.bed DHS_sites.LsLL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Chimp and gorilla and orangutan
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sGGG.locations.bed DHS_sites.sGGG.bb
source GO.create_bigBed_file all_DHS_sites.glm_analysis.sLLL.locations.bed DHS_sites.sLLL.bb
# --------------------------------------------------------------------------------------------------------------------------------------------------
# Other
# --------------------------------------------------------------------------------------------------------------------------------------------------
source GO.create_bigBed_file all_DHS_sites.glm_analysis.OOOO.locations.bed DHS_sites.OOOO.bb