Alignment with Bowtie 2 — alignmentBowtie2 • pipelineNGS

Aligns FastQ files to a reference genome using Bowtie2, converts the output to BAM, sorts it according to genomic position and indexes the final BAM file.

Usage

alignmentBowtie2(
  file,
  out_name = NULL,
  type = "SE",
  cores = 6,
  index = "/vault/refs/indexes/hg38",
  path_bam = "bam/",
  path_logs = "logs/",
  extra_bowtie2 = "",
  run = TRUE
)

Arguments

file: Character string (single-end) or character vector of length 2 (paired-end) with the file names of the samples to be analysed.
out_name: Character vector, with the same length as fastq_files, indicating the output filenames.
type: Sequence type, one of "SE" (single end) or "PE" (paired end).
cores: Number of threads to use for the analysis.
index: Character indicating the location and basename for the Bowtie2 index.
path_bam: Character indicating the output directory for the bam files.
path_logs: Character indicating the output directory for the logs.
extra_bowtie2: Character containing additional arguments to be passed to bowtie2 alignment call.
run: Logical indicating whether to run the alignment (for testing purposes). Default: TRUE

Value

Writes out_name.raw.bam in path_bam. Also generates a log for the alignment (sample.alignment.log) in your path_logs.

Examples

if (FALSE) {
alignmentBowtie2(file=paste0(path, "fastq/NL1_h3k27ac_sample.fastq.gz"),
                 suffix_fastq=".fastq.gz",
                 type="SE",
                 index="/vault/refs/indexes/hg38",
                 path_bam=paste0(path, "bam/"),
                 path_logs=paste0(path, "logs/"),
                 cores=6,
                 run=FALSE)
}