doBowtie2: Read alignment using the Bowtie v2 aligner

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Read alignment using the Bowtie v2 aligner based on [1].

Usage

  doBowtie2(...)
  ## S3 method for class 'FastqDataSet'
doBowtie2(dataSet, reference, ..., verbose=FALSE)

Arguments

dataSet, df	A FastqDataSet.
reference	A FastaReferenceFile or a Bowtie2IndexSet specifying the genome reference to align the FASTQ reads to.
...	Additional arguments passed to Bowtie2Alignment.
verbose	See Verbose.

Value

Returns a BamDataSet.

Author(s)

Henrik Bengtsson

References

[1] Bowtie2, John Hopkins University, 2013. http://bowtie-bio.sourceforge.net/bowtie2/

See Also

For more details, see Bowtie2Alignment.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.