ciri2: Running CIRI v2 tool for circRNAs prediction

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

Running CIRI v2 tool for circRNAs prediction

Description

This function executes the docker container ciri2 where CIRI v2.0.6 is installed and it provides the list of circRNAs predicted from a RNA-Seq experiment. For CIRI 2 tool detail refer to: "Gao, Y., Zhang, J., & Zhao, F. (2017). Circular RNA identification based on multiple seed matching. Brief Bioinform. 2018 Sep 28;19(5):803-810."

Usage

ciri2(
  group = c("sudo", "docker"),
  scratch.folder,
  sam.file,
  genome.file,
  annotation.file = NA,
  max.span = 2e+05,
  stringency.value = c("high", "low", "zero"),
  quality.threshold = 10,
  threads = 1
)

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 file from BWA
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
max.span	an integer reporting the maximum spanning distance of a circRNA (default = 200000 bp)
stringency.value	the selected stringency level of the analysis. Three possible options are available: "high" (high stringency, default), in which CIRI2 only provides circRNAs supported by more than 2 distinct Paired Chiastic Clipping (PCC) signals; "low" (low stringency), CIRI2 only provides circRNAs supported by more than 2 junction reads; "zero", CIRI2 provides all circRNAs regardless junction read counts or PCC signals
quality.threshold	integer indicating the threshold for mapping quality of each segment of junction reads (default=10)
threads	integer indicating the number of threads used for the analysis (default=1)

Value

The list of CIRI 2 predicted circRNAs

Author(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 

    #retrieve the example data
    system("wget https://sourceforge.net/projects/ciri/files/CIRI2/CIRI_v2.0.6.zip") #retrieve the example data
    system("unzip CIRI_v2.0.6.zip")

    #running ciri2 function
    ciri2(group="docker", scratch.folder="/data/scratch", sam.file=paste(getwd(),"/CIRI_v2.0.6/data/sample.sam", sep=""), genome.file=paste(getwd(),"/CIRI_v2.0.6/data/chr1.fa", sep=""), annotation.file="", max.span=200000, stringency.value="high", quality.threshold=10, threads=1)

## End(Not run)

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