Table Of Contents¶

Omics Pipe
- Introduction
- Installation
- Tutorials
- Online Resources
- Site Navigation
About Omics Pipe
- Available Pipelines
- Users
- Developers
- Contact
Using Omics Pipe
- Requirements
- Installation
- Usage
- Running Omics Pipe on Amazon Web Services (AWS)
- Tutorial
- Version history
- Documentation
- Questions
OmicsPipe on the Amazon Cloud (AWS EC2) Tutorial
- Step 1: Create an AWS Account
- Step 2 (Mac or Linux): Install StarCluster and download config/plugins
- Step 2 (Windows): Load the the OmicsPipe on AWS docker image on your machine
- Step 3: Configure StarCluster
- Step 4: Create AWS Volumes
- Step 5: Launch the Cluster
- Step 6: Upload data to the cluster
- Step 7: Run the test pipelines
- Step 8: Run the pipelines with your own data
- Installing extra software
- To build your own docker image
- Add storage > 1TB to the cluster using LVM (for advanced users)
- Add storage > 1TB to the cluster using RAID 0 (for advanced users)
- Backing up your data to S3
Omics Pipe Tutorial
- Installation
- Before Running Omics Pipe: Configuring Parameters File
- Running Omics Pipe
- Running Omics Pipe with the Test Data and Parameters
- Running Omics Pipe with your own data
Omics Pipe Tutorial – Configuring the Parameter File
- Example Omics Pipe Parameter File
- Explanation of Variables in Omics Pipe Parameter File
  - RNAseq Count Based Pipeline
  - RNAseq Tuxedo Pipeline
Omics Pipe Tutorial – Creating a Custom Pipeline Script
- Designing the structure of the pipeline
- Creating the script
- Updating your parameters file
Omics Pipe Tutorial – Adding a New Module (Tool)
- 1. Create a Bash script
- 2. Create a Python module
- 3. Add custom Python module to your custom pipeline
- 4. Add new parameters to parameters file
- 5. Create Custom Module Directory
- 6. Run your pipeline
Omics Pipe Available Pipelines
- RNA-seq (Tuxedo)
- RNA-seq(Anders 2013)
- Whole Exome Sequencing (GATK)
- Whole Genome Sequencing (GATK)
- Whole Genome Sequencing (MUTECT)
- ChIP-seq (MACS)
- ChIP-seq (HOMER)
- Breast Cancer Personalized Genomics Report- RNAseq
- TCGA Reanalysis Pipeline - RNAseq
- TCGA Reanalysis Pipeline - RNAseq Counts
- miRNAseq Counts (Anders 2013)
- miRNAseq (Tuxedo)
- All Available Modules
Reference Databases Needed
- All Pipelines
  - Genome
  - Reference Annotation Files
- Reference Data for Cancer Reporting Scripts (RNAseq cancer, TCGA pipelines)
  - In your omics pipe installation directory under omics_pipe/scripts/reporting/ref place the files.
  - In your omics pipe installation directory under omics_pipe/scripts/reporting/data place the remaining files.
- References for Variants (RNA-seq cancer, RNA-seq cancer TCGA, WES and WGS pipelines)
  - You can put these files in any directory. You will point to their location in the parameters file.
  - In your omics pipe installation directory under omics_pipe/scripts/reporting/ref place these files.
- WES Pipeline
- ChIP-seq Pipelines
- SNPiR Pipelines (RNA-seq cancer and RNA-seq cancer TCGA pipelines)
Third Party Software Dependencies
- R Packages Needed
- RNA-seq (Tuxedo)
- RNA-seq (Anders 2013)
- Whole Exome Sequencing (GATK)
- Whole Genome Sequencing (GATK)
- Whole Genome Sequencing (MUTECT)
- ChIP-seq (MACS)
- ChIP-seq (HOMER)
- Breast Cancer Personalized Genomics Report- RNAseq
- TCGA Reanalysis Pipeline - RNAseq
- TCGA Reanalysis Pipeline - RNAseq Counts
- miRNAseq Counts (Anders 2013)
- miRNAseq (Tuxedo)
System Requirements
RNA-seq Tuxedo Modules
- FASTQC
- TopHat
- Cufflinks
- Cuffmerge
- Cuffmergetocompare
- Cuffdiff
- R Summary Report
RNA-seq Count Based Modules
- FASTQC
- STAR Aligner
- HTSEQ-count
- R Summary Report - DESEQ2
Breast Cancer Personalized Genomics Report- RNAseq
- FASTQC
- STAR Aligner
- HTSEQ-count
- RSEQC
- Fusion Catcher
- BWA/SNPiR
- Intogen
- OncoRep Cancer Report
TCGA Reanalysis Pipeline - RNAseq
- TCGA Download
- FASTQC
- STAR Aligner
- HTSEQ-count
- RSEQC
- Fusion Catcher
- BWA/SNPiR
- Intogen
- OncoRep Cancer Report
RNA-seq Count Based Modules- TCGA
- TCGA Download
- FASTQC
- STAR Aligner
- HTSEQ-count
- R Summary Report - DESEQ2
miRNA-seq Tuxedo Modules
- CutAdapt
- Fastq Length Filter
- FASTQC
- TopHat
- Cufflinks
- Cuffmerge
- Cuffmergetocompare
- Cuffdiff
- R Summary Report
miRNA-seq Count Based Modules
- CutAdapt
- Fastq Length Filter
- FASTQC
- STAR Aligner
- HTSEQ
- R Summary Report - DESEQ2
ChIP-seq Modules – HOMER
- FASTQC
- ChIP trim
- Bowtie
- Read Density -HOMER
- Peak Detection - HOMER
- Peak Annotation & Visualization - HOMER
- Find Motifs - HOMER
ChIP-seq Modules – MACS
- FASTQC
- ChIP trim
- Bowtie
- MACS
Whole Genome and Whole Exome Sequencing Modules
- FASTQC
- BWA-MEM
- PICARD Mark Duplicates
- GATK Preprocessing
  - WES
  - WGS
- GATK Variant Discovery
- GATK Variant Filtering
Whole Genome Sequencing (MUTECT)
- FASTQC
- BWA-MEM
- MUTECT
All Available Modules
Version History
- 1.1.3 (2014/08/22)
- 1.1.2b (2014/08/05)
  - New Features
  - Bug Fixes
- 1.1.0 (2014/07/09)
- 1.0.16 (2014/07/01)
  - New Features
  - Bug Fixes
- 1.0.15 (2014/06/20)
  - New Features
Copyright & License
- Omics Pipe