Generating rsem-star genome index

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

rsemstarIndex(
  group = c("sudo", "docker"),
  genome.folder = getwd(),
  ensembl.urlgenome = NULL,
  ensembl.urlgtf = 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 for STAR will be located

ensembl.urlgenome,

a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest

ensembl.urlgtf,

a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest

threads,

a number indicating the number of cores to be used from the application

Value

The index of the reference genomic sequence for STAR analysis

Author

Raffaele Calogero

Examples

if (FALSE) {
    #running rsemstar index for human
    rsemstarIndex(group="sudo",genome.folder="/data/scratch/hg38star",
    ensembl.urlgenome=
    "ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz",
    ensembl.urlgtf=
    "ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz",
    threads=24)

    #running rsemstar index for mouse
    rsemstarIndex(group="docker",genome.folder="/data/scratch/mm10star",
    ensembl.urlgenome="ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz",
    ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-87/gtf/mus_musculus/Mus_musculus.GRCm38.87.gtf.gz",
    threads=24)

}