A function to estimate counts using Salmon quasi-alignment

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")
)

Arguments

group,

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

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: "se" or "pe" respectively for single end and pair end sequencing. Strandness is inferred by salmon.

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: "none", "forward", "reverse" respectively for non strand selection, reverse for Illumina strandness protocols, reverse for ACCESS Illumina protocol

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
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")
}