bowtie2: Running bowtie2

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

Running bowtie2

Description

This function executes the docker container bowtie2

Usage

bowtie2(
  group = c("sudo", "docker"),
  fastq.folder = getwd(),
  scratch.folder = "/data/scratch",
  genome.folder,
  seq.type = c("se", "pe"),
  strandness = c("none", "forward", "reverse"),
  threads = 1
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
fastq.folder	a character string indicating where gzip fastq files are located
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
genome.folder	a character string indicating the folder where the indexed reference genome for STAR is located. IMPORTANT the present function only suport genomic indexes made using ensembl genom and the corresponding gtf
seq.type	a character string indicating the type of reads to be trimmed. Two options: "se" or "pe" respectively for single end and pair end sequencing
strandness	a character string indicating the type ofsequencing protocol used for the analysis. Three options: "none", "forward", "reverse" respectively for non strand selection, forward for Illumina strandness protocols, reverse for ACCESS Illumina protocol
threads	a number indicating the number of cores to be used from the application

Value

sorted.bam, sorted.bam.bai

Author(s)

Raffaele Calogero

Examples

## Not run: 
    #downloading fastq files
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 bowtie nostrand pe
bowtie2(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch/",
         genome.folder="/data/genomes/hg38bowtie2/", seq.type="pe", strandness="none",
         threads=8)


## End(Not run)

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