Preparing the bed file required by starchip to detect circular RNAs on paired-end sequences

This function prepare the genome bed file for starchip, the GTF must be the one used by starChimeric

starChipIndex(group = c("sudo", "docker"), genome.folder = getwd())

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

genome.folder,

a character string indicating the folder where the indexed reference genome for STAR is located.

Value

the bed files of the reference genome for STARChip analysis

Author

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy

Examples

if (FALSE) {
    starChipIndex(group="docker", genome.folder="/data/genomes/hg38star")
}