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

Author

Nicola Licheri and Giulio Ferrero

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")

}