A function to create a Salmon pseudo reference

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

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

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

Examples

if (FALSE) {
    #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)
    
}