Multi-omics reveals principles of gene regulation and pervasive non-productive transcription in the human cytomegalovirus genome

This upload contains the scripts as well as the source code of the programs written throughout the study, as well as the mapped reads-data to fully generate all the figures and tables for the accompanying publication. The bash-script titled 1_start.bash starts the whole analysis pipeline. However, each line is commented and could therefore be copy and pasted into the command line to execute just single steps of the pipeline. System requirements: Java 1.8,