salmonIndex.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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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. |
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) }