sncRNA: Running small RNA-seq single-end reads alignment and...

Description Usage Arguments Value Author(s) Examples

View source: R/sncRNA.R

Description

This function executes the docker container where BWA is installed. BWA is a read alignment package that efficiently align short sequencing reads against a large reference sequence. Alignment is performed against annotations of human small RNAs. Read count is performed by GenomicAlignments R package and custom Python and bash commands.

Usage

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sncRNA(group = c("sudo", "docker"), fastq.folder = getwd(),
  scratch.folder, mode, reference, threads = 1, mb.version = NULL,
  mb.species = NULL)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

fastq.folder,

a character string indicating where trimmed fastq files are located

scratch.folder,

a character string indicating the scratch folder where docker container will be mounted

mode,

a character string indicating the required type of analysis. Compatible analyses mode are "miRNA" and "ncRNA". In "miRNA" analysis mode, the version ("mb.version" argument) and species prefix ("mb.species" argument) of miRBase are required. This mode require also the "reference" argument. In the "ncRNA" mode only the "reference" argument is required.

reference,

a character string indicating the path to the reference fasta file used to create the BWA index

threads,

a number indicating the number of cores to be used from the application

mb.version,

a character string indicating the required version of miRBase database. Visit ftp://mirbase.org/pub/mirbase/ to select the proper version id.

mb.species,

a character string indicating the three-letter prefix of a species annotated in miRBase (e.g. "hsa" for human miRNAs). Please refer to http://www.mirbase.org/help/genome_summary.shtml to obtain the proper species prefix.

Value

read count files:

Author(s)

Giulio Ferrero

Examples

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## Not run: 
    #downloading fastq files
    system("wget http://130.192.119.59/public/test_R1.fastq.gz")

    #running miRNAs quantification pipeline
    bwaIndex(group="docker", genome.folder="/data/genomes", mb.version="22", mb.species="hsa", mode="miRNA")
    sncRNA(group="docker", fastq.folder=getwd(), scratch.folder="/data/scratch", mode="miRNA", reference="/data/genome/hairpin_hsa_miRBase_22.fa", threads=8, mb.version="22", mb.species="hsa")
    
    #running non miRNA ncRNAs quantification pipeline
    bwaIndex(group="docker", genome.folder="/data/genomes/", rc.version="9.0", rc.species="Homo sapiens", length=80, mode="ncRNA")
    sncRNA(group="docker", fastq.folder=getwd(), scratch.folder="/data/scratch", mode="ncRNA", reference="/data/genome/ncRNA_Homo_sapiens_RNA_Central_9_len_80.fa", threads=8)


## End(Not run)

kendomaniac/docker4seq documentation built on Nov. 18, 2018, 11:12 a.m.