This function prepare the genome bed file for starchip, the GTF must be the one used by starChimeric
a character string. Two options: sudo or docker, depending to which group the user belongs
a character string indicating the folder where the indexed reference genome for STAR is located.
three files: dedup_reads.bam, which is sorted and duplicates marked bam file, dedup_reads.bai, which is the index of the dedup_reads.bam, and dedup_reads.stats, which provides mapping statistics
Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy
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