Annotating RSEM gene.results using ENSEMBL gtf and refGenome CRAN package

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)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

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 "rsemstar" function. In this folder is present the GTF used for by RSEM

Value

one file: annotated_genes.results, which is the annotated version of gene.results.

Author

Raffaele Calogero

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")
    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")
}