Running Star to detect chimeric transcripts on paired-end sequences

This function executes STAR to detect chimeric transcripts

starChimeric(
  group = c("sudo", "docker"),
  fastq.folder = getwd(),
  scratch.folder,
  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 integer indicating the minimal length of the overlap of a read to the chimeric element

chimJunctionOverhangMin,

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

Value

the set of chimeric transcripts identified by STAR chimeric

Author

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

Examples

if (FALSE) {
    #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)

}