ciriAS: Running CIRI_AS tool for circRNAs structure prediction

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

Running CIRI_AS tool for circRNAs structure prediction

Description

This function executes the docker container docker4circ where CIRI_AS is installed

Usage

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(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 

    #Download the example data
    system("wget https://sourceforge.net/projects/ciri/files/CIRI-AS/test_data_CIRI_AS.zip/download")

    system("mv download test_data_CIRI_AS.zip")
    system("unzip test_data_CIRI_AS.zip")

 # Run the ciriAS function
ciriAS(group = "docker", scratch.folder="/data/scratch", sam.file=paste(getwd,"/test_data_CIRI_AS/test.sam",sep=""), ciri.file=paste(getwd,"/test_data_CIRI_AS/test.ciri", genome.file=paste(getwd,"/test_data_CIRI_AS/chr1.fa", sep=""), annotation.file = paste(getwd,"/test_data_CIRI_AS/chr1.gtf", sep="")

## End(Not run)

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