wrapperSalmon.Rd
This function executes a docker that produces as output the transcripts count file generated by Salmon quasi-alignment and convert it the same format of isoforms.result of RSEM
wrapperSalmon( group = c("sudo", "docker"), scratch.folder, fastq.folder, index.folder, threads = 24, seq.type = c("se", "pe"), adapter5, adapter3, min.length, strandness = c("none", "forward", "reverse") )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs |
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scratch.folder, | a character string indicating the path of the scratch folder |
fastq.folder, | a character string indicating the folder where input data are located and where output will be written |
index.folder, | a character string indicating the folder where transcriptome index was created with salmonIndex. |
threads, | a number indicating the number of cores to be used from the application |
seq.type, | a character string indicating the type of reads to be generated by the sequencer. Two options: |
adapter5, | a character string indicating the fwd adapter |
adapter3, | a character string indicating the rev adapter |
min.length, | a number indicating minimal length required to return a trimmed read |
strandness, | a character string indicating the type ofsequencing protocol used for the analysis. Three options: |
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 wrapperSalmon(group="docker", scratch.folder="/scratch/users/rcaloger/", fastq.folder=getwd(), index.folder="/archive/home/rcaloger/data/seqbox/salmonIndex.R", threads=24, seq.type="pe", adapter5="AGATCGGAAGAGCACACGTCTGAACTCCAGTCA", adapter3="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", min.length=40, strandness="none") }