omics_pipe
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
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
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
Reference Data for Cancer Reporting Scripts (RNAseq cancer, TCGA pipelines)
References for Variants (RNA-seq cancer, RNA-seq cancer TCGA, WES and WGS pipelines)
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
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)
1.1.0
(2014/07/09)
1.0.16
(2014/07/01)
1.0.15
(2014/06/20)
Copyright & License
Omics Pipe
omics_pipe
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