Running CircHunter circRNA backsplicing sequence reconstruction module

This function executes the docker container circhunter by running the circRNA back-splicing sequence reconstruction module of CircHunter starting from a set of circRNAs. For CircHunter algorithm detail please refer to: https://github.com/carlo-deintinis/circhunter/tree/master/CircHunter.

circrnaBSJunctions(
  group = c("sudo", "docker"),
  scratch.folder,
  circrna.data,
  exon.data,
  assembly = "hg19"
)

Arguments

group,

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

a character string indicating the scratch folder where docker container will be mounted
circrna.data,

string indicating the path to the list of circRNAs
exon.data,

string indicating the path to the exon annotation file
assembly,

string indicating the reference human genome assembly. Compatible assemblies: hg19 (default), hg18, hg38, mm9, mm10, rn6, dm6, ce11.

Value

A fasta file reporting the sequence of circRNA back-splice junctions

Examples

if (FALSE) {

    #retrieve the example data
    system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip")
    system("unzip master.zip")

    #running the circrnaBSJunctions function
    circrnaBSJunctions(group="docker", scratch.folder="/data/scratch", circrna.data=paste(getwd(),"/circhunter-master/CircHunter/toyexample/toy_circRNA", sep=""), exon.data=paste(getwd(),"/circhunter-master/CircHunter/toyexample/toy_genome", sep=""), assembly="hg19")

}