tophat: Calls the TopHat executable to align input reads

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

Description

Calls the TopHat executable to align input reads.

Usage

 ## Default S3 method:
tophat(bowtieRefIndexPrefix, reads1=NULL, reads2=NULL, gtf=NULL,
  transcriptomeIndexPrefix=NULL, mateInnerDist=NULL, mateStdDev=NULL, optionsVec=NULL,
  ..., outPath="tophat/", command="tophat", verbose=FALSE)
 ## Default S3 method:
tophat1(..., command="tophat")
 ## Default S3 method:
tophat2(..., command="tophat2")

Arguments

bowtieRefIndexPrefix	A character string specifying the Bowtie2 reference index prefix.
reads1	(required) A vector of FASTQ pathnames of reads.
reads2	(optional; paired-end only) A vector of FASTQ pathnames of mate reads.
gtf	(optional) A GTF pathname.
mateInnerDist, mateStdDev	(optional; paired-end only) The expected mean and standard deviation of the inner distance between mate pairs.
optionsVec	Vector of named options to pass to the executable.
...	(Not used)

.

outPath	Directory where result files are written.
command	The name of the executable.
verbose	See Verbose.

Support for compressed input files

TopHat (>= 1.3.0), which was released June 2011, handles FASTQ files that have been compressed by gzip (or bzip2) [1]. If not supported, this method will give an informative error message about it.

Author(s)

Henrik Bengtsson, Taku Tokuyasu

References

[1] TopHat - A spliced read mapper for RNA-Seq, 2015. http://ccb.jhu.edu/software/tophat/

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