For description of code please download and open either the .html file or knit the .Rmd file.
Trimming and mapping of fastq files was run with the multimap_pipe.nf pipeline and modules in the nextflow_pipeline folder. Conda environment build is also found in that folder.
Results/output are viewable and able to download in the csv file.
Graphing and stats analysis code is separate and in: 19.1.22_multimapping_graphs_stats_script.R