doTopHat2: Read alignment using the TopHat v2 aligner

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

Description

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

Usage

  doTopHat2(...)
  ## S3 method for class 'FastqDataSet'
doTopHat2(dataSet, reference, transcripts, ..., verbose=FALSE)

Arguments

dataSet, df	A FastqDataSet.
reference	A FastaReferenceFile or a Bowtie2IndexSet specifying the genome reference to align the FASTQ reads to.
transcripts	A GtfDataFile or NULL specifying known transcripts and/or gene model annotations.
...	Additional arguments passed to TopHat2Alignment.
verbose	See Verbose.

Value

Returns a BamDataSet.

Author(s)

Henrik Bengtsson

References

[1] TopHat - A spliced read mapper for RNA-Seq, 2015. http://ccb.jhu.edu/software/tophat/
[2] Trapnell et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012.

See Also

For more details, see TopHat2Alignment.

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