Running xenome, https://github.com/data61/gossamer/

This function executes the docker container bwa1 where BWA is installed BWA is a read alignment package that efficiently align short sequencing reads against a large reference sequence This aligner provides optimal results with DNA-seq data

xenome(
  group = c("sudo", "docker"),
  fastq.folder = getwd(),
  scratch.folder = "/data/scratch",
  xenome.folder,
  seq.type = "pe",
  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

xenome.folder,

a character string indicating the folder where the indexed reference genomes generated by xenome are locates

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

threads,

a number indicating the number of cores to be used from the application

Value

ambiguous, both, neither, hs and mm fastq.gz files. xeno_hs_R1.fastq.gz and xeno_hs_R2.fastq.gz are fastq file free of mouse reads and are used for further analysis.

Author

Raffaele Calogero

Examples

if (FALSE) {
    #downloading examples 1 million reads of mcf7 exome mixed with 1 million of mouse derived by human exome capturing
    system("wget http://130.192.119.59/public/hs1m_mm1m_R1.fastq.gz")
    system("wget http://130.192.119.59/public/hs1m_mm1m_R2.fastq.gz")
    #running xenome
    xenome(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
    xenome.folder="/data/scratch/hg19.mm10", seq.type="pe",
    threads=24)

}