circrnaQuantification: Running CircHunter circRNA quantification module

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

Running CircHunter circRNA quantification module

Description

This function executes the docker container circhunter by running the circRNA quantification module of CircHunter to quantify the level of expression of a set of circRNA BS sequences in a given RNA-Seq experiment. For CircHunter algorithm detail please refer to: https://github.com/carlo-deintinis/circhunter/tree/master/CircHunter.

Usage

circrnaQuantification(
  group = c("sudo", "docker"),
  scratch.folder,
  rnaseq.data,
  backsplicing_junctions.data,
  hc.params
)

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
rnaseq.data	string indicating the path to the fastq file of the RNA-Seq dataset to analyse
backsplicing_junctions.data	string indicating the path to the fasta file of the circRNA back-splicing sequences to search in the RNA-Seq dataset
hc.params	vector of six parameters to set the analysis. The element of the vector indicate in order: the k-mer size, the thread number, the dimension of the hash table, the dimension of the collision list, the number of k-mers that must be matched to the sequence to consider the sequence itself as represented in the RNA-Seq data, and the number of perfect matches required in the k-mer to consider it matched to a sequence.

Value

A count table reporting the number of RNA-Seq reads supporting specific 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")
    system("gzip ./circhunter-master/CircHunter/data/test_rna-seq.fastq.gz")

    #running the circrnaQuantification function
    circrnaQuantification(group="docker", scratch.folder="/data/scratch", rnaseq.data=paste(getwd,"/circhunter-master/CircHunter/data/test_rna-seq.fastq.gz", sep=""), backsplicing_junctions.data=paste(getwd,"/circhunter-master/CircHunter/data/CRC_circRNA_backsplicing_sequences.fasta", sep=""), hc.params=c(27, 40, 1000000, 1000000, 17, 30))


## End(Not run)

kendomaniac/docker4seq documentation built on April 8, 2024, 5:39 p.m.