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