bowtie2Index: Generating bowtie2 genome index

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

Generating bowtie2 genome index

Description

This function executes the docker container bowtie2 where bowtie2-2.2.9 is 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

bowtie2Index(
  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 Bowtie 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 indexed Bowtie genome reference sequence

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #running rsemstar index for human
    bowtie2Index(group="docker",genome.folder="/data/scratch/hg38bowtie2",
    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=8)


## End(Not run)

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