dup_rate <- function(bamfile){
# not a working example
gtf <- "genes.gtf"
stranded <- 2
paired <- FALSE
threads <- 4
bamDuprm <- markDuplicates(dupremover="bamutil",bamfile,
path="/opt/bamUtil-master/bin",rminput=FALSE)
dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
return(dm)
}
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