A function to annotate salmon output

This function executes a docker that convert the transcripts count file generated by Salmon quasi-alignment in the same format of isoforms.result, geness.result of RSEM and add the ENSEMBL GTF based annotation

salmonAnnotation(group = c("sudo", "docker"), fastq.folder, index.folder)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

fastq.folder,

a character string indicating the folder where input data are located and where output will be written, it should contain quant.sf file generated by salmonCounts

index.folder,

a character string indicating the folder where Salmon transcriptome index was created with salmonIndex.

Author

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

Examples

if (FALSE) {
system("wget http://130.192.119.59/public/test_R1.fastq.gz")
system("wget http://130.192.119.59/public/test_R2.fastq.gz")
library(docker4seq)
#running salmonCounts
library(docker4seq)
wrapperSalmon(group="docker", scratch.folder="/data/scratch/",
              fastq.folder=getwd(), index.folder="/data/genomes/hg38salmon",
              threads=8, seq.type="pe", adapter5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
              adapter3="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", min.length=40, strandness="none")
#converting in a format identical to rsem isoform.results
salmonAnnotation(group="docker", fastq.folder=getwd(),
                 index.folder="/data/genomes/hg38salmon")

}