In aiminy/ChipSeq: An R Package for Performing ChipSeq Analysis In One Step

The tutorial to use ChipSeq

Set up environment

Install the following softares firstly:

1. ngsplt(https://github.com/shenlab-sinai/ngsplot)

2. MACS(https://github.com/taoliu/MACS)

3. ChipSeq(https://github.com/aiminy/ChipSeq)

#To download

git clone https://github.com/aiminy/ChipSeq

#To build 

R CMD build --resave-data ChipSeq

if knitr is not installed, please install it by performing the following step

R -e 'install.packages("knitr", dependencies = TRUE,repos = "http://cran.rstudio.org",lib="/nethome/axy148/R/lib64/R/library")'


#To Install
R CMD INSTALL ChipSeq_0.0.1.tar.gz -l ~/R/lib64/R/library/

Peak Call and Annotation

input.file.dir="/projects/scratch/bbc/Project/Danny_chip/Alignment/BWA/"
output.file.dir="/scratch/projects/bbc/aiminy_project/
genome="Hs"

library(ChipSeq)
PeakCallAndAnnotation(input.file.dir,output.file.dir,genome)

Bam files sorting, index and Visualization

• Run ChipSeq to perform one-setp analysis for ChipSeq related data

input.file.dir="/projects/scratch/bbc/Project/Danny_chip/Alignment/BWA/"
output.file.dir="/scratch/projects/bbc/aiminy_project/
genome="Hs"

BamFileSortIndexVisualization(input.file.dir,output.file.dir,genome)

Perform the above steps in one streamlined procedure

You run this job on the linux cluster(pegasus)

```{bash eval=FALSE}

sh ~/R/lib64/R/library/ChipSeq/bin/BashRun.sh /projects/scratch/bbc/Project/Danny_chip/Alignment/BWA/ /scratch/projects/bbc/aiminy_project/ "Hs"

To check output

ls -lrth /scratch/projects/bbc/aiminy_project/

You will find the follwing latest directories that was created with a timestamp

For example,

Peak call is located in

/scratch/projects/bbc/aiminy_project/ReadBam_at_2016-12-01-18-58-57_PeakCall/

Peak call is located in

/scratch/projects/bbc/aiminy_project/ReadBam_at_2016-12-01-18-58-57_PeakAnnotation/

Peak call is located in

/scratch/projects/bbc/aiminy_project/ReadBam_at_2016-12-01-18-58-57_visualization/ ```

aiminy/ChipSeq documentation built on May 12, 2019, 3:37 a.m.