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
 
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© Copyright 2014, Kathleen Fisch, Ph.D.. Last updated on Jan 28, 2015.

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