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GO.step05.run_galaxy_coverage_tool.MANUAL
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GO.step05.run_galaxy_coverage_tool.MANUAL
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# ################################################################################################################################################################################################################
# GO.step05.run_galaxy_coverage_tool.MANUAL
#
# 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)
# ################################################################################################################################################################################################################
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Must be done manually
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Step 1: Upload the following files to Galaxy ( https://usegalaxy.org/ )
all_DHS_sites.before_coverage_filter.bed
all_DHS_sites.before_coverage_filter.maf
Step 2: Run "MAF Coverage Stats" (located in the "Fetch Alignments / Sequences" section)
Interval File all_DHS_sites.before_coverage_filter.bed
MAF Source Alignments in Your History
all_DHS_sites.before_coverage_filter.maf
Type of Output Coverage by Region
Save file as: all_DHS_sites.before_coverage_filter.galaxy_coverage_output.txt
Coverage file format
column 1: chromosome
column 2: start
column 3: end
column 4: genome
column 5: number of nucleotides
column 6: number of gaps