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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# # 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")
# system(paste("tree", prj))
# # now there is a project directory, create another alignment directory.
# project_rnsq(prjd = prj, alnd = "alignment2")
# ./project1
# ├── alignment
# │   ├── command_log.txt
# │   ├── res_hisat2
# │   │   └── failalign
# │   └── res_stringtie
# │       ├── ballgown
# │       ├── gff
# │       ├── mgff
# │       └── tab
# ├── alignment2
# │   ├── res_hisat2
# │   │   └── failalign
# │   └── res_stringtie
# │       ├── ballgown
# │       ├── gff
# │       ├── mgff
# │       └── tab
# ├── fastq
# └── qa

shkonishi/rskoseq documentation built on June 24, 2018, 6:19 a.m.