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uauy edited this page Oct 16, 2015 · 12 revisions

Loading Virtual Machine

The expVIP Virtual Machine (VM) allows you to analyse your own RNA-Seq expression experiments locally.

Requirements

The virtual machine requires:

  • VirtualBox, version 5 or newer.
  • 6GB of RAM
  • A 64-bit operating system running on an x86_64 architecture. (Intel, AMD)
  • 10GB of free space.

Default data

The default values loaded in the virtual machine are available in this link. These correspond to the wheat data from Borrill, Ramirez-Gonzalez and Uauy, 2015 (submitted).

You can get a virtual machine with expVIP installed with either the wheat data preloaded or an empty database for your analysis here.

Available VMs

  1. expVIPNoData.ova This VM is ready to use, but it has no data on it. You can load a custom set of RNA-seq reads, transcriptome reference and metadata.
  2. expVIPwithWheatData.ova This has all the data loaded from www.wheat-expression.com. You can add your own data and compare it with the values of publicly available experiments.

Setup shared folders

To load your custom RNA-seq experiments, you have to setup a shared folder with your input files. This shared folder will contain the data and information required by the VM to implement expVIP and it provides the "connection" between your computer and the VM. This shared folder should include:

  1. RNA-seq reads: as fastq or fq.gz files.
  2. Transcriptome reference: currently only the cdna fasta file from ensembl is supported.
  3. Metadata: this includes two separate files; one factor file and one metadata file ([explained here] (https://github.com/homonecloco/expvip-web/wiki/LoadingMetadata)).

Some important information:

  • The shared folder must contain one sub-folder per each set of RNA-seq reads. So for example if you wish to analyse data from three samples, you will need three sub-folders (one each with the individual sample RNA-seq reads)
  • Each RNA-seq sub-folder must be named with the same accession number that you use in your metadata (see [here] (https://github.com/homonecloco/expvip-web/wiki/LoadingMetadata)).
  • If you wish to add your own wheat data to that previously provided in www.wheat-expression.com you will need to include sub-folders with your RNA-seq reads and then modify the metadata files: default_metadata.txt and FactorOrder.tsv which are provided in the expVIPwithWheatData.ova or can be downloaded here. Additional factors and metadata can be added at the end of these files following similar nomenclature as that already present in the files.

Loading the virtual machine

Download the ova virtual machine and double click it. Virtual Box will open it. Accept the default options.

If The virtual machine is not loaded, go to the menu File and click Import appliance. Open the .ova you want to use

Availabe VMs:

  • expVIP.ova expVIP is installed with an empty database. This VM requires to setup your own samples.
  • expVIPwithWheatData.ova expVIP is installed with the wheat expression data, transcriptome reference and metadata. This VM allows the inclusion of additional samples to integrate with the previously analysed wheat data.
  1. On the Oracle VM VirtualBox Manager select expVIP and click on the settings button alt text
  2. Click in Shared folders alt text
  3. Add a new folder alt text
  4. Search the Folder path with the experiments and the files with the metadata alt text alt text
  5. Select the folder alt text
  6. Make sure that the Auto-mount option is selected. alt text
  7. Accept the settings alt text

Starting the virtual machine

Select expVIP from the VM list and press start. alt text

NOTES

kallisto is included as part of the virtual machine and is free for non-commercial use. However, it requires a license for commercial use. The distribution of kallisto, with the corresponding license is included in ~/software/ in the VM.

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