CRI RNAseq 2018

RNA-Seq Analysis Pipeline based on CRI HPC system

CAUTION

THIS PACKAGE IS LARGE, PLEASE DO NOT DOWNLOAD IT TO YOUR HOME DIRECTORY
USE OTHER LOCATION LIKE /gpfs/data/bioinformatics/username

Dataset

The RNA-seq data used in this tutorial are from the project CRI-BIO-646-BMB-RKeenan.

File description

This repository contains the following items:

• docs/README.html - the main tutorial documentation
• CRI-BIO-646/ - folder accommodating all data (i.e., metadata file, configuration file, sequencing data folder, and references folder) for running this pipeline
• README.md - this description file
• SRC/ - automatic pipelines for RNA-seq analysis

Prerequisites

• R
• CRAN
• Bioconductor
• Python 3
• BigDataScript

Installing

# CAUTION

**THIS PACKAGE IS LARGE, PLEASE DO NOT DOWNLOAD IT TO YOUR HOME DIRECTORY**  
**USE OTHER LOCATION LIKE /gpfs/data/bioinformatics/username**

# download the package via 'wget'
wget ftp://logia.cri.uchicago.edu/bioinformatics/tutorials/Nov2018/CRI-BIO-646-BMB-RKeenan.tgz
# Or, copy the package directly from HPC
cp /gpfs/data/bioinformatics/shared/tutorials/Nov2018/CRI-BIO-646-BMB-RKeenan.tgz .

# uncompress the tarball file
tar -zxvf CRI-BIO-646-BMB-RKeenan.tgz

# change working directory to the package directory
cd CRI-BIO-646-BMB-RKeenan

# load modules
$ module purge;module load gcc udunits python/3.6.0 R/3.5.0; module update

# This step is optional but it will install all necessary R packages ahead.
# In case the pipeline was terminated due to the failure of R package installation later when running the pipeline.
$ Rscript --vanilla SRC/R/util/prerequisite.packages.R

# create directories and generate all necessary scripts
$ bash Build_RNAseq.CRI-BIO-646.sh

# run the entire pipeline with just this command
$ bash Submit_CRI-BIO-646-BMB-RKeenan.sh

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

For the versions available, see the tags on this repository.

Authors

• Wen-Ching Chan - Initial work - Wen-Ching

See also the list of contributors who participated in this project.

License

This project is licensed under the LGPLv3 License - see the LICENSE file with a copy for details

Acknowledgments

• Thank Kyle Hernandez for providing a private Git repository in the begining of this project
• Thank Riyue Bao for providing tutorial dataset, figures, and the pipeline in the Perl version
• Thank PurpleBooth for providing the templates of README.md & CONTRIBUTING.md