rsemannoByGtf.Rd
This function executes the docker container annotate.1, where refGenome is used to annotated gene.results and isoforms.results outputs from RSEM using ENSEMBL GTF annotation
rsemannoByGtf(group = "docker", rsem.folder = getwd(), genome.folder)
group, | a character string. Two options: |
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rsem.folder, | a character string indicating where gene.results file is located |
genome.folder, | a character string indicating the folder for the genome reference used for mapping and counting with |
one file: annotated_genes.results, which is the annotated version of gene.results.
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) #running rsemannoByGtf rsemannoByGtf(group="docker", rsem.folder=getwd(), genome.folder="/data/scratch/hg38star") }