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- ._t2t_transposable-elements-main
  
  312 Bytes
- t2t_transposable-elements-main
  - ._.DS_Store
    
    120 Bytes
  - ._.DS_Store.gz
    
    212 Bytes
  - ._CutnRun_analyses
    
    212 Bytes
  - ._Data_visualization
    
    212 Bytes
  - ._README.md
    
    212 Bytes
  - ._README.md.gz
    
    263 Bytes
  - ._RepeatMasker_compilation_pipeline
    
    212 Bytes
  - ._Repeat_annotations
    
    212 Bytes
  - ._Transcriptional_analyses
    
    212 Bytes
  - ._Transduction_analyses
    
    212 Bytes
  - CutnRun_analyses
    - ._.DS_Store
      
      120 Bytes
    - ._.DS_Store.gz
      
      212 Bytes
    - ._KmerFilteringPipeline-CutnRun_JULY042021_SHoyt.txt
      
      275 Bytes
    - ._README.md
      
      275 Bytes
  - Data_visualization
    - ._.DS_Store.gz
      
      212 Bytes
    - ._Circos_plots
      
      212 Bytes
    - ._Deeptools_heatmaps
      
      212 Bytes
    - ._Methylation_boxplots
      
      212 Bytes
    - ._Methylation_heatmaps
      
      212 Bytes
    - ._Methylation_metaplots
      
      212 Bytes
    - ._Phylogenic_relationships
      
      212 Bytes
    - ._README.md.gz
      
      319 Bytes
    - ._RepeatsAbundance_CASK_plots
      
      212 Bytes
    - ._Rideogram_plots
      
      212 Bytes
    - ._SequenceID_dotplots
      
      212 Bytes
    - ._Transduction_frequency_plots
      
      212 Bytes
    - ._Transduction_synteny_plots
      
      212 Bytes
    - ._Xist_PhaseMethylation
      
      212 Bytes
    - Circos_plots
      - ._CreateCIRCOSPlots_circos.sh.gz
        
        212 Bytes
    - Deeptools_heatmaps
      - ._.DS_Store.gz
        
        212 Bytes
      - ._PlotHeatmaps-SplitStrands_DeepTools2.R.gz
        
        212 Bytes
      - ._PlotHeatmaps-SplitStrands_DeepTools2_3'fixed_SE.R.gz
        
        212 Bytes
      - ._PlotHeatmaps_DeepTools2.R.gz
        
        212 Bytes
      - ._PlotHeatmaps_DeepTools2_KmerCoverage.R
        
        275 Bytes
    - Methylation_boxplots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._L1_Subfamilies-FLvNot_Methylation-CG-BoxPlots_ggplot.Rmd.gz
        
        212 Bytes
      - ._SVA_Subfamilies-FLvNot_Methylation-CG-BoxPlots_ggplot.Rmd.gz
        
        212 Bytes
    - Methylation_heatmaps
      - ._.DS_Store.gz
        
        212 Bytes
      - ._PlotMethylationHeatmaps_Deeptools2.R.gz
        
        212 Bytes
      - ._PlotMethylationHeatmaps_Deeptools2_3'fixed.R.gz
        
        212 Bytes
    - Methylation_metaplots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._CEN3_methylMetaplot_withnorm.Rmd.gz
        
        212 Bytes
      - ._HORedgeMethylationMetaplot_ggplot.Rmd.gz
        
        212 Bytes
      - ._SST1MethylationMetaplot_ggplot.Rmd.gz
        
        212 Bytes
      - ._TELOcompositeMethylationMetaplot_ggplot.Rmd.gz
        
        212 Bytes
    - Phylogenic_relationships
      - ._.DS_Store.gz
        
        212 Bytes
      - ._PhylogeneticAnalysisTemplate_RAxML.sh.gz
        
        212 Bytes
    - RepeatsAbundance_CASK_plots
      - ._repeatsCountsCASK-RM_ggplot.Rmd.gz
        
        212 Bytes
      - ._tableS20generate_dplyr.Rmd.gz
        
        212 Bytes
    - Rideogram_plots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._KaryotypeHeatmapIdeograms_RIdeogram.R.gz
        
        212 Bytes
      - ._TransductionKaryotypeHeatmapIdeograms_Rideogram.R.gz
        
        212 Bytes
    - SequenceID_dotplots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._README.md.gz
        
        212 Bytes
    - Transduction_frequency_plots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._Transductionper1MB_ggplot.R.gz
        
        212 Bytes
    - Transduction_synteny_plots
      - ._.DS_Store.gz
        
        212 Bytes
      - ._TransductionLinkage_Rideogram.R.gz
        
        212 Bytes
    - Xist_PhaseMethylation
      - ._.DS_Store.gz
        
        212 Bytes
      - ._CHM13-XistPhaseMethylation_ggplot.Rmd.gz
        
        212 Bytes
      - ._HG002-XistPhaseMethylation_ggplot.Rmd.gz
        
        212 Bytes
  - RepeatMasker_compilation_pipeline
    - ._.DS_Store
      
      120 Bytes
    - ._.DS_Store.gz
      
      212 Bytes
    - ._README_RM_comp
      
      275 Bytes
    - ._RMcomp.pl
      
      275 Bytes
    - ._addValue.py.gz
      
      212 Bytes
    - ._columnExtract4.py.gz
      
      212 Bytes
    - ._columnExtractRM.py.gz
      
      212 Bytes
    - ._replaceComp.py.gz
      
      212 Bytes
    - ._rm_filter.py.gz
      
      212 Bytes
    - ._rm_to_bed_expanded.py.gz
      
      212 Bytes
  - Repeat_annotations
    - ._.DS_Store
      
      120 Bytes
    - ._.DS_Store.gz
      
      212 Bytes
    - ._GAP_identification
      
      212 Bytes
    - ._LTRharvest_and_TransposonPSI
      
      212 Bytes
    - ._Primate_Genome_Analysis
      
      212 Bytes
    - ._README.md
      
      275 Bytes
    - ._Repeatmasker_and_polishing
      
      212 Bytes
    - ._Repeatmodeler
      
      212 Bytes
    - GAP_identification
      - ._.DS_Store.gz
        
        212 Bytes
      - ._IdentificationandTRF_of_RMgaps.gz
        
        591 Bytes
    - LTRharvest_and_TransposonPSI
      - ._LTRharvestIndex_genometools.sh.gz
        
        212 Bytes
      - ._LTRharvestRun_genometools.sh.gz
        
        212 Bytes
      - ._RunTransposonCheck_transposonPSI.sh.gz
        
        212 Bytes
    - Primate_Genome_Analysis
      - ._.DS_Store.gz
        
        212 Bytes
      - ._PrimateGenomeSearches_BLAST.sh.gz
        
        212 Bytes
    - Repeatmasker_and_polishing
      - ._.DS_Store.gz
        
        212 Bytes
      - ._README.md.gz
        
        212 Bytes
      - ._RepeatLibrary_T2T-CHM13_RepeatEntries.embl.gz
        
        212 Bytes
      - ._fixRMtoZero.py.gz
        
        212 Bytes
      - ._rm_filter.py.gz
        
        212 Bytes
      - ._rm_to_bed_expanded.py.gz
        
        212 Bytes
    - Repeatmodeler
      - ._BuildDatabase_RepeatModeler.sh.gz
        
        212 Bytes
      - ._RepeatModelSearch_RepeatModeler.sh.gz
        
        212 Bytes
  - Transcriptional_analyses
    - ._.DS_Store
      
      120 Bytes
    - ._.DS_Store.gz
      
      212 Bytes
    - ._CASK_analysis
      
      212 Bytes
    - ._README.md
      
      275 Bytes
    - ._ReadandLocus_KmerFilteringPipeline-PROseq-RNAseq
      
      275 Bytes
    - ._Repeatmasking_reads
      
      212 Bytes
    - ._chm13v1.0_seqLengths.genome.gz
      
      212 Bytes
    - CASK_analysis
      - ._.DS_Store.gz
        
        212 Bytes
      - ._cask_preprocessing_dplyr.Rmd.gz
        
        212 Bytes
    - Repeatmasking_reads
      - ._.DS_Store.gz
        
        212 Bytes
      - ._RepeatMasking_ReadSets.gz
        
        589 Bytes
  - Transduction_analyses
    - ._.DS_Store
      
      120 Bytes
    - ._.DS_Store.gz
      
      212 Bytes
    - ._README.md.gz
      
      514 Bytes
    - ._tsdfinder.V1.0.pl
      
      275 Bytes
t2t_transposable-elements-main
- .DS_Store
  
  6.1 kB
- .DS_Store.gz
  
  549 Bytes
- CutnRun_analyses
  - .DS_Store
    
    6.1 kB
  - .DS_Store.gz
    
    206 Bytes
  - KmerFilteringPipeline-CutnRun_JULY042021_SHoyt.txt
    
    3.0 kB
  - README.md
    
    187 Bytes
- Data_visualization
  - .DS_Store.gz
    
    737 Bytes
  - Circos_plots
    - CreateCIRCOSPlots_circos.sh.gz
      
      158 Bytes
  - Deeptools_heatmaps
    - .DS_Store.gz
      
      206 Bytes
    - PlotHeatmaps-SplitStrands_DeepTools2.R.gz
      
      547 Bytes
    - PlotHeatmaps-SplitStrands_DeepTools2_3'fixed_SE.R.gz
      
      558 Bytes
    - PlotHeatmaps_DeepTools2.R.gz
      
      338 Bytes
    - PlotHeatmaps_DeepTools2_KmerCoverage.R
      
      986 Bytes
  - Methylation_boxplots
    - .DS_Store.gz
      
      206 Bytes
    - L1_Subfamilies-FLvNot_Methylation-CG-BoxPlots_ggplot.Rmd.gz
      
      1.8 kB
    - SVA_Subfamilies-FLvNot_Methylation-CG-BoxPlots_ggplot.Rmd.gz
      
      1.3 kB
  - Methylation_heatmaps
    - .DS_Store.gz
      
      206 Bytes
    - PlotMethylationHeatmaps_Deeptools2.R.gz
      
      1.4 kB
    - PlotMethylationHeatmaps_Deeptools2_3'fixed.R.gz
      
      1.7 kB
  - Methylation_metaplots
    - .DS_Store.gz
      
      206 Bytes
    - CEN3_methylMetaplot_withnorm.Rmd.gz
      
      2.4 kB
    - HORedgeMethylationMetaplot_ggplot.Rmd.gz
      
      2.2 kB
    - SST1MethylationMetaplot_ggplot.Rmd.gz
      
      2.2 kB
    - TELOcompositeMethylationMetaplot_ggplot.Rmd.gz
      
      2.3 kB
  - Phylogenic_relationships
    - .DS_Store.gz
      
      206 Bytes
    - PhylogeneticAnalysisTemplate_RAxML.sh.gz
      
      276 Bytes
  - README.md.gz
    
    211 Bytes
  - RepeatsAbundance_CASK_plots
    - repeatsCountsCASK-RM_ggplot.Rmd.gz
      
      2.2 kB
    - tableS20generate_dplyr.Rmd.gz
      
      1.9 kB
  - Rideogram_plots
    - .DS_Store.gz
      
      206 Bytes
    - KaryotypeHeatmapIdeograms_RIdeogram.R.gz
      
      1.3 kB
    - TransductionKaryotypeHeatmapIdeograms_Rideogram.R.gz
      
      1.3 kB
  - SequenceID_dotplots
    - .DS_Store.gz
      
      206 Bytes
    - README.md.gz
      
      577 Bytes
  - Transduction_frequency_plots
    - .DS_Store.gz
      
      206 Bytes
    - Transductionper1MB_ggplot.R.gz
      
      1.5 kB
  - Transduction_synteny_plots
    - .DS_Store.gz
      
      206 Bytes
    - TransductionLinkage_Rideogram.R.gz
      
      1.8 kB
  - Xist_PhaseMethylation
    - .DS_Store.gz
      
      206 Bytes
    - CHM13-XistPhaseMethylation_ggplot.Rmd.gz
      
      2.9 kB
    - HG002-XistPhaseMethylation_ggplot.Rmd.gz
      
      2.0 kB
- README.md
  
  289 Bytes
- README.md.gz
  
  211 Bytes
- RepeatMasker_compilation_pipeline
  - .DS_Store
    
    6.1 kB
  - .DS_Store.gz
    
    206 Bytes
  - README_RM_comp
    
    3.6 kB
  - RMcomp.pl
    
    2.4 kB
  - addValue.py.gz
    
    289 Bytes
  - columnExtract4.py.gz
    
    212 Bytes
  - columnExtractRM.py.gz
    
    354 Bytes
  - replaceComp.py.gz
    
    174 Bytes
  - rm_filter.py.gz
    
    288 Bytes
  - rm_to_bed_expanded.py.gz
    
    361 Bytes
- Repeat_annotations
  - .DS_Store
    
    6.1 kB
  - .DS_Store.gz
    
    513 Bytes
  - GAP_identification
    - .DS_Store.gz
      
      206 Bytes
    - IdentificationandTRF_of_RMgaps.gz
      
      307 Bytes
  - LTRharvest_and_TransposonPSI
    - LTRharvestIndex_genometools.sh.gz
      
      228 Bytes
    - LTRharvestRun_genometools.sh.gz
      
      149 Bytes
    - RunTransposonCheck_transposonPSI.sh.gz
      
      205 Bytes
  - Primate_Genome_Analysis
    - .DS_Store.gz
      
      206 Bytes
    - PrimateGenomeSearches_BLAST.sh.gz
      
      182 Bytes
  - README.md
    
    2.7 kB
  - Repeatmasker_and_polishing
    - .DS_Store.gz
      
      206 Bytes
    - README.md.gz
      
      909 Bytes
    - RepeatLibrary_T2T-CHM13_RepeatEntries.embl.gz
      
      27.0 kB
    - fixRMtoZero.py.gz
      
      411 Bytes
    - rm_filter.py.gz
      
      288 Bytes
    - rm_to_bed_expanded.py.gz
      
      359 Bytes
  - Repeatmodeler
    - BuildDatabase_RepeatModeler.sh.gz
      
      146 Bytes
    - RepeatModelSearch_RepeatModeler.sh.gz
      
      126 Bytes
- Transcriptional_analyses
  - .DS_Store
    
    6.1 kB
  - .DS_Store.gz
    
    360 Bytes
  - CASK_analysis
    - .DS_Store.gz
      
      206 Bytes
    - cask_preprocessing_dplyr.Rmd.gz
      
      3.0 kB
  - README.md
    
    420 Bytes
  - ReadandLocus_KmerFilteringPipeline-PROseq-RNAseq
    
    4.1 kB
  - Repeatmasking_reads
    - .DS_Store.gz
      
      206 Bytes
    - RepeatMasking_ReadSets.gz
      
      432 Bytes
  - chm13v1.0_seqLengths.genome.gz
    
    231 Bytes
- Transduction_analyses
  - .DS_Store
    
    6.1 kB
  - .DS_Store.gz
    
    206 Bytes
  - README.md.gz
    
    163 Bytes
  - tsdfinder.V1.0.pl
    
    73.2 kB

t2t_transposable-elements-main.zip