starChimeric: Running Star to detect chimeric transcripts on paired-end...

Description Usage Arguments Value Author(s) Examples

View source: R/starChimeric.R

Description

This function executes STAR to detect chimeric transcripts

Usage

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starChimeric(group = c("sudo", "docker"), fastq.folder = getwd(),
  scratch.folder = "/data/scratch", genome.folder, threads = 1,
  chimSegmentMin = 20, chimJunctionOverhangMin = 15)

Arguments

group,

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

fastq.folder,

a character string indicating where gzip fastq files are located

scratch.folder,

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

genome.folder,

a character string indicating the folder where the indexed reference genome for STAR is located.

threads,

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

chimSegmentMin,

is a positive value indicating the minimal lenght of the overlap of a read to the chimeric element

chimJunctionOverhangMin,

is a positive value indicating the minimum overhang for a chimeric junction

Value

three files: dedup_reads.bam, which is sorted and duplicates marked bam file, dedup_reads.bai, which is the index of the dedup_reads.bam, and dedup_reads.stats, which provides mapping statistics

Author(s)

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy

Examples

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## Not run: 
    #downloading fastq files
    system("wget http://130.192.119.59/public/test_R1.fastq.gz")
    system("wget http://130.192.119.59/public/test_R2.fastq.gz")
    #running star2step nostrand pe
    starChimeric(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
    genome.folder="/data/scratch/hg38star", threads=8, chimSegmentMin=20, chimJunctionOverhangMin=15)


## End(Not run)

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