alignmentBowtie2: Alignment with Bowtie 2

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Alignment with Bowtie 2

Description

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

## Not run: 
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)

## End(Not run)

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.