RNASeq Virtual Land
From Array Suite Wiki
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.
Part 1: Build an Internal Land from RNA-seq Raw Data
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.
When the job is done, several sub folders will show up as shown in the screenshot below:
ALV files are available in sub folders:
Create a new Internal Land
After generating ALV files, an ArrayServer administrator should go to Land -> Tools -> Create Land to create an internal Land.
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.
Add sample metadata
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.
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:
Below is an example of the Sample Metadata file that would match the demo Land data from the RNAseq tutorial data.
In the Manage Sample Meta Data page, users can click Add/Replace to add metadata table:
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.
Part II: Create a VirtualLand combining your Internal Land and CCLE
To create a virtual land, go to Tools | Create Virtual Land".
Select multiple Lands and enter a virtual land name.
The created virtual land will be listed in the land collection (right panel).
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.
Change the Primary and secondary grouping
put the following command when creating a virtual land
The Primary Grouping and the Secondary grouping options will be assigned to Source Land and Tissue column directly in the newly created virtual Land.
More setting about virtual land could be found on our wiki: Settings_for_Creating_Virtual_Land