starChimeric.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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 |
the set of chimeric transcripts identified by STAR chimeric
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) }