star2steps.Rd
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 )
group, | a character string. Two options: |
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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. |
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 |
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
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) }