rsubread_featurecount_script.R

library(Rsubread)


args <- commandArgs(trailingOnly = TRUE)

if (length(args) != 5) {
    cat("Usage: Rscript featureCounts_script.R <bamFilesDirectory> <gtfFile> <isPairedEnd> <numThreads> <outputCSV>\n")
    quit(status = 1)
}



filepath <- args[1]
gtfFile <- args[2]
isPairedEnd <- as.logical(args[3])
numThreads <- as.numeric(args[4])
outputCSV <- args[5]



if (!grepl("/$", filepath)) {
    filepath <- paste0(filepath, "/")
}


filenames <- list.files(path = filepath, pattern = "\\.bam$", full.names = TRUE)


if (length(filenames) == 0) {
    cat("No BAM files found in the specified directory.\n")
    quit(status = 1)
}

# Running featureCounts
featurecounts <- featureCounts(files = filenames, 
                               annot.ext = gtfFile, 
                               isGTFAnnotationFile = TRUE, 
                               nthreads = numThreads, 
                               isPairedEnd = isPairedEnd, 
                               countReadPairs = TRUE)

write.csv(featurecounts$counts, file = outputCSV, row.names = TRUE)

cat("FeatureCounts analysis completed successfully.\n")