Create a bigWig from the output of bowtie2

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

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

Raffaele Calogero

Examples

if (FALSE) {
    #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)

}