Function to prepare the CircHunter reference annotations

This function executes the docker container circhunter by running the circRNA classification 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.

circrnaPrepareFiles(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  assembly = "hg19",
  version = NULL
)

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

data.folder,

a character string indicating the data folder where the output files will be saved

assembly,

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

version,

Ensembl database version used for the analysis. If no version number is provided, the last version is considered

Value

Two tab-delimited tables reporting the exons and the transcript isoforms annotations of an user-selected human genome assembly

Author

Nicola Licheri and Giulio Ferrero

Examples

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

    #running the circrnaPrepareFiles function
    circrnaPrepareFiles(group="docker", scratch.folder="/data/scratch", data.folder="/data/output", assembly="hg19")

}