genomics.isi.edu
Quickstart – RSeq Workflow | USC GENOMICS
https://genomics.isi.edu/brainspan/documents/quickstart/quickstart-rseq-workflow
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. Quickstart – RSeq Workflow. In this quick start guide we will show you how to set up the virtual machine and run the RSeq workflow using a sample dataset. Download the Virtual Machine. Uncompress the image using the following command.
genomics.isi.edu
Source Code | USC GENOMICS
https://genomics.isi.edu/brainspan/downloads/source-code
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. Alignment tool to map the sequencing dataset to reference sequences. Sort cut split.sh. Keep one map for one read, and then cut the valid columns and split the mapping results by chromosome. Generate Quality Control report. Python prog...
genomics.isi.edu
Running RSeq Workflow | USC GENOMICS
https://genomics.isi.edu/brainspan/documents/running-rseq-workflow
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. This part will map the fastq/fasta RNA-Seq data to genome and transcriptome, then produce QC report of sequencing data, SNP calling results, wig file for Genome browser, expression level and reads counts for gene/exon/splicing junction.
genomics.isi.edu
Quickstart – DE Workflow | USC GENOMICS
https://genomics.isi.edu/brainspan/documents/quickstart/quickstart-de-workflow
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. Quickstart – DE Workflow. In this quick start guide we will show you how to set up the virtual machine and run the DE workflow using a sample dataset. Download the Virtual Machine. Uncompress the image using the following command.
genomics.isi.edu
iSeqTools Workshop at ASHG 2014 | USC GENOMICS
https://genomics.isi.edu/iseqtools-workshop-ashg-2014
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. ISeqTools Workshop at ASHG 2014. ISeqTools to Demistify the Cloud and Genomics Analysis for Researchers Seeking Ways to Analyze High-Throughput DNA Sequencing Data. Introduction to iSeqTools workshop. By R Jay Mashl. By Mary Kate Wing.
genomics.isi.edu
Workflow Running Mode | USC GENOMICS
https://genomics.isi.edu/brainspan/workflow-construction
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. NOTE: Brain Span project finished in 2012. These are legacy pages. The Pegasus Workflow Management Service was adopted to manage the workflow’s operations. It helps workflow execute in different kinds of different environments incl...
genomics.isi.edu
RSeqFlow | USC GENOMICS
https://genomics.isi.edu/rnaseq
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. The description of the pipeline and instructions for running it can be found on google code. Proudly powered by WordPress.
genomics.isi.edu
Virtual Machine | USC GENOMICS
https://genomics.isi.edu/brainspan/downloads/virtual-machine
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. The Virtual Machine consists of two virtual disks. Debian 64 Bit OS – Linux 64 bit Operating System. Brain – The Brain disk consists of (Atlas workflow, Rhesus workflow, and DE workflow). Proudly powered by WordPress.
genomics.isi.edu
Installation/Configuration | USC GENOMICS
https://genomics.isi.edu/brainspan/documents/userguide
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. A 64 bit processor. Any 64 bit OS. A disk drive with 300GB of free space. A minimum of 16GB of RAM if using PerM mapper OR 4GB RAM if using Bowtie mapper. How to configure the VM. Run VM using VirtualBox 4. Run VM using KVM. The comput...
genomics.isi.edu
Quickstart | USC GENOMICS
https://genomics.isi.edu/brainspan/documents/quickstart
Decoding the Genome on the Cloud. ISeqTools Workshop at ASHG 2014. Pegasus GT-FAR on AWS. UNIX Shell Running Mode. Reference Annotation Files Downloads for Several Species. Quickstart – RSeq Workflow. Quickstart – DE Workflow. Running Rhesus RSeq Workflow. Ting Chen’s Lab. Proudly powered by WordPress.