Nadel-et-al.-2015 This repository contains scripts for the data processing and analysis employed in "RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships."

Hard coded path for file names has been left in code for complete explanation of data analysis

Name		Name	Last commit message	Last commit date
Determining RNA Strand and Minus10 files		Determining RNA Strand and Minus10 files
Figure 2 - rDNA figure with Zentner Histone marks		Figure 2 - rDNA figure with Zentner Histone marks
Figure 3 - enrichment depletion with Perm testing		Figure 3 - enrichment depletion with Perm testing
Figure 4 - nucleotide ratio figure		Figure 4 - nucleotide ratio figure
Figure 5 - Relationship with Transcription		Figure 5 - Relationship with Transcription
Figure 6 - LASSO plot data compilation		Figure 6 - LASSO plot data compilation
Figure S3 - Gene Body Intersection with Skewing		Figure S3 - Gene Body Intersection with Skewing
Figure S5 - Methylation figure		Figure S5 - Methylation figure
Figure S7 - Removal Protein Expression plot		Figure S7 - Removal Protein Expression plot
Peak Calling		Peak Calling
README.md		README.md
RNAseq analysis		RNAseq analysis
Zentner removeDupsFromFastQ Perl Script		Zentner removeDupsFromFastQ Perl Script

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