wrapperSalmon: A function to estimate counts using Salmon quasi-alignment

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function to estimate counts using Salmon quasi-alignment

Description

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

Usage

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(s)

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

Examples

## Not run: 
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")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.