The following loads one of the available NGS workflow templates (here RIBO-Seq) into the user’s current working directory. At the moment, the package includes workflow templates for RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Templates for additional NGS applications will be provided in the future. The sample data are described here.

library(systemPipeRdata)
genWorkenvir(workflow = "riboseq", bam = TRUE)
setwd("riboseq")

Download latest version of this tutorial

In case there is a newer version of this tutorial, download its systemPipeRIBOseq.Rmd source and open it in your R IDE (e.g. vim-r or RStudio).

download.file("https://raw.githubusercontent.com/tgirke/systemPipeRdata/master/vignettes/systemPipeRIBOseq.Rmd", 
    "systemPipeRIBOseq.Rmd")

Load packages and sample data

The systemPipeR package needs to be loaded to perform the analysis steps shown in this report (Girke , 2014). The package allows users to run the entire analysis workflow interactively or with a single command while also generating the corresponding analysis report. For details see systemPipeR's main vignette.

library(systemPipeR)

In the workflow environments generated by genWorkenvir all data inputs are stored in a data/ directory and all analysis results will be written to a separate results/ directory, while the systemPipeRIBOseq.Rmd script and the targets file are expected to be located in the parent directory. The R session is expected to run from this parent directory. Additional parameter files are stored under param/.

To work with real data, users want to organize their own data similarly and substitute all test data for their own data. To rerun an established workflow on new data, the initial targets file along with the corresponding FASTQ files are usually the only inputs the user needs to provide.

If applicable users can load custom functions not provided by systemPipeR. Skip this step if this is not the case.

source("systemPipeRIBOseq_Fct.R")

Experiment definition provided by targets file

The targets file defines all FASTQ files and sample comparisons of the analysis workflow.

targetspath <- system.file("extdata", "targets.txt", package = "systemPipeR")
targets <- read.delim(targetspath, comment.char = "#")[, 1:4]
targets
##                       FileName SampleName Factor SampleLong
## 1  ./data/SRR446027_1.fastq.gz        M1A     M1  Mock.1h.A
## 2  ./data/SRR446028_1.fastq.gz        M1B     M1  Mock.1h.B
## 3  ./data/SRR446029_1.fastq.gz        A1A     A1   Avr.1h.A
## 4  ./data/SRR446030_1.fastq.gz        A1B     A1   Avr.1h.B
## 5  ./data/SRR446031_1.fastq.gz        V1A     V1   Vir.1h.A
## 6  ./data/SRR446032_1.fastq.gz        V1B     V1   Vir.1h.B
## 7  ./data/SRR446033_1.fastq.gz        M6A     M6  Mock.6h.A
## 8  ./data/SRR446034_1.fastq.gz        M6B     M6  Mock.6h.B
## 9  ./data/SRR446035_1.fastq.gz        A6A     A6   Avr.6h.A
## 10 ./data/SRR446036_1.fastq.gz        A6B     A6   Avr.6h.B
## 11 ./data/SRR446037_1.fastq.gz        V6A     V6   Vir.6h.A
## 12 ./data/SRR446038_1.fastq.gz        V6B     V6   Vir.6h.B
## 13 ./data/SRR446039_1.fastq.gz       M12A    M12 Mock.12h.A
## 14 ./data/SRR446040_1.fastq.gz       M12B    M12 Mock.12h.B
## 15 ./data/SRR446041_1.fastq.gz       A12A    A12  Avr.12h.A
## 16 ./data/SRR446042_1.fastq.gz       A12B    A12  Avr.12h.B
## 17 ./data/SRR446043_1.fastq.gz       V12A    V12  Vir.12h.A
## 18 ./data/SRR446044_1.fastq.gz       V12B    V12  Vir.12h.B



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