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)



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


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


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


if (FALSE) { system("wget") system("wget") 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") }