rsemannoByGtf: Annotating RSEM gene.results using ENSEMBL gtf and refGenome...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

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

Description

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

Usage

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(s)

Raffaele Calogero

Examples

## Not run: 
    #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")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.