tophat2: tophat2

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run tophat2.

Usage

tophat2(fq1, fq2, output.dir, sample.name, ref.gtf, bowtie.idx, tophat_thread_number=4, build.transcriptome.idx=FALSE, run.cmd=TRUE, mc.cores=1)

Arguments

fq1	Path to read1 fastq files
fq2	Path to read2 fastq files
output.dir	Output directory
sample.name	A character vector for the sample names
ref.gtf	Path to reference gtf file
bowtie.idx	Path to directory with bowtie indexes and a prefix for the bowtie indexes
build.transcriptome.idx	A parameter value for –transcriptome-index in tophat2. A transcriptome index and the associated data files (the original GFF file) can be thus reused for multiple TopHat runs with this option, so these files are only created for the first run with a given set of transcripts. (default=FALSE)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
tophat_thread_number	A parameter value for -p in tophat2. A numeric value of the number of threads (default: 4)

Details

TopHat is a program that aligns RNA-Seq reads to a genome to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.

Value

Aligned BAM files

References

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

See Also

https://ccb.jhu.edu/software/tophat/manual.shtml

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.