circrnaBSJunctions: Running CircHunter circRNA backsplicing sequence...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Running CircHunter circRNA backsplicing sequence reconstruction module

Description

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.

Usage

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(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 

    #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")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.