salmonIndex: A function to create a Salmon pseudo reference

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

A function to create a Salmon pseudo reference

Description

This function executes the Salmon docker that produces as output a transcripts index file.

Usage

salmonIndex(
  group = c("sudo", "docker"),
  index.folder,
  ensembl.urltranscriptome,
  ensembl.urlgtf,
  k = 31
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
index.folder	a character string indicating the folder where transcriptime index will be created.
ensembl.urltranscriptome	a character string indicating the URL from ENSEMBL ftp for the transcripts fasta file of interest
ensembl.urlgtf	a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest
k	a number indicating the k-mers length, 31 eems to work well for reads of 75bp or longer, but you might consider a smaller k if dealing with shorter reads.

Author(s)

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit University of Torino Italy

Examples

## Not run: 
    #running salmonIndex mouse
    salmonIndex(group="docker", index.folder=getwd(), 
    ensembl.urltranscriptome="ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz",
    ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/Mus_musculus.GRCm38.90.gtf.gz", 
    k=31)
    #running salmonIndex human
    library(docker4seq)
    salmonIndex(group="docker", index.folder=getwd(), 
           ensembl.urltranscriptome="ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz",
           ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/Homo_sapiens.GRCh38.90.gtf.gz", 
           k=31)
    

## End(Not run)

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