xenome.Rd
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 )
group, | a character string. Two options: |
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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: |
threads, | a number indicating the number of cores to be used from the application |
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.
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) }