Running CIRCexplorer2 parse command for circRNAs prediction from STAR or BWA alignment output

This function executes the circexplorer2 docker container which parses the fusion file generated by STAR or BWA and extracts circRNA coordinates

CIRCexplorer2(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  fusion.file,
  used.aligner = c("STAR", "BWA")
)

Arguments

group,

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

scratch.folder,

a string indicating the scratch folder where docker container will be mounted

data.folder,

a string indicating the path of the output folder

fusion.file,

a string indicating the path of the fusion file. If the used aligner was BWA, the fusion file is the resulting sam file, whereas the used aligner was STAR, the fusion file is the Chimeric.out.junction file

used.aligner,

a string indicating the aligner used to generate the junctions.file. Supported aligners are STAR and BWA