RNASeq Virtual Land

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Land users are often interested in exploring data across multiple Lands, or comparing internal data with public OmicSoft Lands. Virtual Lands can present data from multiple Lands in a single location, by creating links between multiple Array Lands built with the same Genome and Gene Model. By creating a Virtual Land, users can search and compare across multiple Lands, seeing expression, mutation, copy number, and comparison data.

This page will demonstrate creation of an Internal Land from the RNASeq output from our RNASeq Analysis Tutorial, and how to create a Virtual Land combining this Land with OmicSoft's CCLE Land.

Contents

Part 1: Build an Internal Land from RNA-seq Raw Data

Input Dataset

For this demonstration, we will use the RNASeq_Tutorial RNA-seq tutorial dataset, starting with the fastq files. The full dataset is available on the SRA archives GSM958729 SRR521461-521463 and GSM958745 SRR521522-521524.

Run RNASeq Pipeline to generate ALVs

The simplest way to create Land ALV files (the input data type for Lands), users can run the RNA-Seq pipeline to generate all ALVs for building a Land. One option in this function is to generate ALV files for RNA-seq expression, mutation, exon junction, and fusion data.

RNA Seq Pipeline ALVs.png

When the job is done, several sub folders will show up as shown in the screenshot below:

RNAseq ALV outputs.png

ALV files are available in sub folders:

ALVs subfolder.png

Create a new Internal Land

Tips.pngOnly ArrayServer Administrators can create new Lands, but they can grant user permissions to others to maintain individual Lands.


After generating ALV files, an ArrayServer administrator should go to Land -> Tools -> Create Land to create an internal Land.

Create land.png

Additional Land Configuration settings can be found here.

Publish to the new Land

After creating a Land, users with appropriate Land access can publish new ALVs from the RNA-seq pipeline. Go to Land -> Tools -> Publish To Land to publish all ALVs generated in previous steps to the Land.

Publish to land.png

Add sample metadata

Warning.png WARNING: Please see This page for restrictions on metadata column names.

Once ALV files are published, users need to Manage Land Sample Metadata for visualization. Data cannot be viewed in the Sample Distribution view if Metadata have not been registered in the Land. Add sample metadata in Land Tab | Manage | Samples | Manage Sample Meta Data.

Tips.pngIf Manage Sample Meta Data is in grey (as in the screenshot below), you need to ask admin to change the Land permissions for you.


Needadminnew.png

The meta data table is required to have Sample ID, Subject ID, Primary Grouping, and Secondary Grouping columns exactly the way it was defined in the land.cfg file. Users can view the information that was provided in the land.cfg file by going to Manage | Show Land Statistics:

Showlandstatistics.png

Below is an example of the Sample Metadata file that would match the demo Land data from the RNAseq tutorial data.

Design metadata.png

In the Manage Sample Meta Data page, users can click Add/Replace to add metadata table:

Add metadata.png

If you want users to be able to open RNA-Seq bam files in the Genome Browser directly from Land Views (Browse Selected Samples, the meta data table needs a "BamFileName" column and the Land configuration needs a few BAM/BAS configuration options.

Explore your new Land

After uploading metadata, the Land views should be available.

Search for a gene of interest to make sure that data and metadata are displayed.

Simple internal land.png

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Part II: Create a VirtualLand combining your Internal Land and CCLE

To create a virtual land, go to Tools | Create Virtual Land".

Tips.pngonly administrators are able to create Virtual Lands.


VirtualLand 1.jpg

Select multiple Lands and enter a virtual land name.

RNAseq internal land.png

The created virtual land will be listed in the land collection (right panel).

Select virtual land.png

Cross Land Search

Open a virtual land and search for a gene. You should see data from the RNAseq tutorial data set, as well as CCLE.

There is a column "Source Land" automatically added to the virtual land when it is created.

VirtualLand RNA CCLE.png

Change the Primary and secondary grouping

put the following command when creating a virtual land

PrimaryGroupingName=SourceLand 
SecondaryGroupName=Tissue

ChangePrimaryGrouping.png

The Primary Grouping and the Secondary grouping options will be assigned to Source Land and Tissue column directly in the newly created virtual Land.

PrimaryGrouping.png

More setting about virtual land could be found on our wiki: Settings_for_Creating_Virtual_Land