bwa.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
bwa( group = c("sudo", "docker"), fastq.folder = getwd(), scratch.folder = "/data/scratch", genome.folder, seq.type = c("se", "pe"), threads = 1, sample.id, circRNA = FALSE )
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 |
genome.folder, | a character string indicating the folder where the indexed reference genome for bwa is located |
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 |
sample.id, | a character string indicating the unique id to be associated to the bam that will be created |
circRNA, | a boolean variable indicating whether the analysis concerns a circRNA prediction or not. |
three files: dedup_reads.bam, which is sorted and duplicates marked bam file, dedup_reads.bai, which is the index of the dedup_reads.bam, and dedup_reads.stats, which provides mapping statistics