omics_pipe
Omics Pipe
Introduction
Installation
Tutorials
Online Resources
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About Omics Pipe
Available Pipelines
Users
Developers
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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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Python Module Index
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o
omics_pipe
omics_pipe.modules.annotate_peaks
omics_pipe.modules.annotate_variants
omics_pipe.modules.bowtie
omics_pipe.modules.BreastCancer_RNA_report
omics_pipe.modules.bwa
omics_pipe.modules.call_variants
omics_pipe.modules.ChIP_trim
omics_pipe.modules.cuffdiff
omics_pipe.modules.cuffdiff_miRNA
omics_pipe.modules.cufflinks
omics_pipe.modules.cufflinks_miRNA
omics_pipe.modules.cufflinks_ncRNA
omics_pipe.modules.cuffmerge
omics_pipe.modules.cuffmerge_miRNA
omics_pipe.modules.cuffmergetocompare
omics_pipe.modules.cuffmergetocompare_miRNA
omics_pipe.modules.custom_R_report
omics_pipe.modules.cutadapt_miRNA
omics_pipe.modules.fastq_length_filter_miRNA
omics_pipe.modules.fastqc
omics_pipe.modules.fastqc_miRNA
omics_pipe.modules.filter_variants
omics_pipe.modules.find_motifs
omics_pipe.modules.fusion_catcher
omics_pipe.modules.GATK_preprocessing_WES
omics_pipe.modules.GATK_preprocessing_WGS
omics_pipe.modules.GATK_variant_discovery
omics_pipe.modules.GATK_variant_filtering
omics_pipe.modules.homer_peaks
omics_pipe.modules.htseq
omics_pipe.modules.htseq_gencode
omics_pipe.modules.htseq_miRNA
omics_pipe.modules.intogen
omics_pipe.modules.macs
omics_pipe.modules.mutect
omics_pipe.modules.peak_track
omics_pipe.modules.picard_mark_duplicates
omics_pipe.modules.read_density
omics_pipe.modules.RNAseq_QC
omics_pipe.modules.RNAseq_report
omics_pipe.modules.RNAseq_report_counts
omics_pipe.modules.RNAseq_report_tuxedo
omics_pipe.modules.rseqc
omics_pipe.modules.snpir_variants
omics_pipe.modules.star
omics_pipe.modules.star_piRNA
omics_pipe.modules.TCGA_download
omics_pipe.modules.tophat
omics_pipe.modules.tophat_miRNA
omics_pipe.modules.tophat_ncRNA
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