rsemstar.Rd
This function executes the docker container rsemstar1, where RSEM is used to calculate gene/isoforms counts using as mapper STAR, Dubin et al. Bioinformatics. 2013 Jan 1;29(1):15-21
rsemstar( group = c("sudo", "docker"), fastq.folder = getwd(), scratch.folder = "/data/scratch", genome.folder, seq.type = c("se", "pe"), strandness = c("none", "forward", "reverse"), threads = 1, save.bam = TRUE )
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. IMPORTANT the present function only suport genomic indexes made using ensembl genom and the corresponding gtf |
seq.type, | a character string indicating the type of reads to be trimmed. Two options: |
strandness, | a character string indicating the type ofsequencing protocol used for the analysis. Three options: |
threads, | a number indicating the number of cores to be used from the application |
save.bam, | a boolean TRUE FALSE to decide if bam files are saved |
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") library(docker4seq) #running rsemstar nostrand pe rsemstar(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch/", genome.folder="/data/genomes/hg38star/", seq.type="pe", strandness="none", threads=8, save.bam = FALSE) }