project_rnsq: Create directory for RNA-seq pipeline

Description Usage Arguments Examples

View source: R/project_rnsq.R

Description

Create Project directories for RNA-seq pipeline using hisat2-stringtie. Then fastq files move to './project/fastq' directory, followning execution of 'rskoseq::rep_hisat2' or 'rskoseq::rep_rsem', for read mapping.

Usage

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project_rnsq(prjd, alnd, algnr)

Arguments

prjd

character: path of a project directory name

alnd

character: path of a alignment directory name, the default is "alignment1"

algnr

character: select an alignment program from "hisat2"(default), "rsem", "others"

Examples

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## Not run: 
# create new project
prj <- "~/pub/sampledata/rnaseq/project1"
project_rnsq(prjd = prj, alnd = "test.h2", algnr = "hisat2")
project_rnsq(prjd = prj, alnd = "test.rsm", algnr = "rsem")

# now there is a project directory, create another alignment directory.
system(paste("tree", prj))


## End(Not run)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.