GitHub - ValentinaBoP/CorvidesSat: Code for the paper "Satellite DNA evolution in Corvides inferred from short and long reads"

Name		Name	Last commit message	Last commit date
Latest commit History 37 Commits
PipeSat		PipeSat
Simulations		Simulations
ABUNDANCE_corvides.sh		ABUNDANCE_corvides.sh
ARRAY_RMSK_assembly_analysis.sh		ARRAY_RMSK_assembly_analysis.sh
ARRAY_sat_corvides.sh		ARRAY_sat_corvides.sh
EMBOSS_palindrome.sh		EMBOSS_palindrome.sh
GCcontent_Figure1.sh		GCcontent_Figure1.sh
LENGTH_distribution_Figure1.sh		LENGTH_distribution_Figure1.sh
PCA_Figure5.sh		PCA_Figure5.sh
QUADRON_satellite.sh		QUADRON_satellite.sh
REPEATEXPLORER_preprocess.sh		REPEATEXPLORER_preprocess.sh
RMDL_pipeline_RE2.sh		RMDL_pipeline_RE2.sh
RMSK_PacBio_reads.sh		RMSK_PacBio_reads.sh
RMSK_landscape.sh		RMSK_landscape.sh
RMSK_reads.sh		RMSK_reads.sh
RNAFold.sh		RNAFold.sh
RPKM_calculation.sh		RPKM_calculation.sh
SAMPLES_Corvus_download.sh		SAMPLES_Corvus_download.sh
SATELLITE_landscape_plots.sh		SATELLITE_landscape_plots.sh
SATELLITE_presence_absence.sh		SATELLITE_presence_absence.sh
abundance_proportions.R		abundance_proportions.R
abundance_sat.R		abundance_sat.R
abundance_sat_lc.R		abundance_sat_lc.R
array_rmsk_assemblies.R		array_rmsk_assemblies.R
filterSatelliteRE2.R		filterSatelliteRE2.R
landscape_plots.R		landscape_plots.R
plotFamiliesRPKM.R		plotFamiliesRPKM.R
presenceSat.R		presenceSat.R
presence_sat_techComp.R		presence_sat_techComp.R
presence_sat_threshold.R		presence_sat_threshold.R
repeatModelerPipeline4.pl		repeatModelerPipeline4.pl
satellite_pipeline_functions.R		satellite_pipeline_functions.R
satellite_pipeline_setup.R		satellite_pipeline_setup.R

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Code for the paper "Satellite DNA evolution in Corvides inferred from short and long reads"

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