Running CIRI_AS tool for circRNAs structure prediction

This function executes the docker container docker4circ where CIRI_AS is installed

ciriAS(
  group = c("sudo", "docker"),
  scratch.folder,
  sam.file,
  ciri.file,
  genome.file,
  annotation.file = NA
)

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

sam.file,

a character string indicating the path to the RNA-Seq alignment SAM/BAM file from BWA

ciri.file,

string indicating the path to the list of circRNAs

genome.file,

a character string indicating the path to the Fasta file of the reference genomic sequence (it should be the same reference indexed for the BWA alignment)

annotation.file,

a character string indicating the path to the GTF/GFF file reporting the reference gene annotations

Value

The function returns the list of alternative circRNAs internal structures

Author

Nicola Licheri and Giulio Ferrero

Examples