rsemstarUscsIndex: Generating rsem-star genome index

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

Generating rsem-star genome index

Description

This function executes the docker container rsem-star1 where RSEM and STAR are installed. The index is created using ENSEMBL genome fasta file. User needs to provide the URL for ENSEMBL genome located in the ENSEMBL ftp

Usage

rsemstarUscsIndex(
  group = c("sudo", "docker"),
  genome.folder = getwd(),
  uscs.urlgenome = NULL,
  uscs.gtf = NULL,
  uscs.urlknownIsoforms = NULL,
  uscs.urlknownToLocusLink = NULL,
  threads = 1
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
genome.folder	a character string indicating the folder where the indexed reference genome will be located
uscs.urlgenome	a character string indicating the URL from uscs download web page for the unmasked genome sequence of interest
uscs.gtf	a character string indicating the path of the GTF file for genome of interest
uscs.urlknownIsoforms	a character string indicating the URL from uscs download web page for the knowisoforms file for genome of interest
uscs.urlknownToLocusLink	a character string indicating the URL from uscs download web page for the knownToLocusLink file for genome of interest
threads	a number indicating the number of cores to be used from the application

Value

The indexed genome reference sequence

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #running rsemstar index for human
    rsemstarUscsIndex(group="sudo",genome.folder="/data/scratch/hg19UCSCstar",
    uscs.urlgenome=
    "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz",
    uscs.gtf=
    "/Users/raffaelecalogero/Desktop/hg19_ucsc.gtf.gz",
    uscs.urlknownIsoforms=
    "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownIsoforms.txt.gz",
    uscs.urlknownToLocusLink=
    "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownToLocusLink.txt.gz",
    threads=24)


## End(Not run)

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