salmonIndex: A function to create a Salmon pseudo reference

Description Usage Arguments Author(s) Examples

View source: R/salmonIndex.R

Description

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

Usage

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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

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## 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 Nov. 8, 2018, 6:49 p.m.