cufflinks: cufflinks

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

Description

A wrapper function to run Cufflinks for mRNA quantitation

Usage

cufflinks(fns.bam, sample.name, output.dir, cufflinks_thread_number=4, cufflinks.gtf="G", ref.gtf, run.cmd=TRUE, mc.cores=1)

Arguments

fns.bam	Path to bam files
output.dir	Output directory
sample.name	A character vector for the sample names
cufflinks.thread.number	A parameter value for -p in Cufflinks. A numeric value of the number of threads (default: 4)
cufflinks.gtf	If you set -G, Output will not include novel genes and isoforms that are assembled. (default: -G)
ref.gtf	Path to reference gtf file
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.

Details

Cufflinks algorithms for transcript assembly and expression quantification are much more accurate with paired-end reads.

Value

mRNA quantification text files

References

http://cole-trapnell-lab.github.io/cufflinks/papers/

See Also

http://cole-trapnell-lab.github.io/cufflinks/

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