Running Star two steps for variant calls

This function executes the two steps STAR as sugested by best practice GATK for calling variants on RNAseq data only PE data are accepted

star2steps(
  group = c("sudo", "docker"),
  fastq.folder = getwd(),
  scratch.folder = "/data/scratch",
  genome.folder,
  groupid,
  threads = 1,
  opossum.preprocessing = FALSE
)

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.

groupid,

a character string to be inserted in the bam as identifier for the sample

threads,

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

opossum.preprocessing,

a boolean TRUE or FALSE to use opossum for RNAseq data preprocessing https://wellcomeopenresearch.org/articles/2-6/v1

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

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
    star2steps(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
    genome.folder="/data/scratch/hg38star", groupid="test", threads=8, opossum.preprocessing=FALSE)

}