deeptoolBwig: Create a bigWig from the output of bowtie2

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

Create a bigWig from the output of bowtie2

Description

This function executes the docker container bowtie2 embedding deeptools the output of bowtie2 sorted.bam is used to generate the bigWig

Usage

deeptoolBwig(
  group = c("sudo", "docker"),
  fastq.folder = getwd(),
  scratch.folder = "/data/scratch",
  threads
)

Arguments

group	a character string. Two options: "sudo" or "docker", depending to which group the user belongs
fastq.folder	a character string indicating where bam, bai files are located
scratch.folder	a character string indicating the scratch folder where docker container will be mounted
threads	a number indicating the number of cores to be used from the application

Value

sorted.bw

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)
deeptoolBwig(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch/", threads=8)


## End(Not run)

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