RNASeq Virtual Land
From Array Suite Wiki
Virtual Land is a virtual link between multiple Array Lands. By creating a virtual land, users can search and compare across multiple lands.This page show workflow to create an internal land with RNASeq data download from RNASeq Analysis section in Omicsoft Tutorial, and how to create a virtual land based on the RNA-seq Land and CCLE Land.
Build Internal Lands with RNASeq Raw Data
Test Dataset is the same one from RNA-Seq tutorial. RNASeq_Tutorial This dataset was run on the Illumina Genome Analyzer platform, and each read is 76bp long. We have selected six SRR run .fastq paired-end files for use in this analysis. The full dataset is available on the SRA archive:
SRR521461-521463 from GSM958729:
SRR521522-521524 from GSM958745:
Run RNASeq Pipeline to generate ALVs
Users could simply run RNA-Seq pipeline to generate all ALVs for building a Land.
When the job is done, several sub folders will show up as shown in the screenshot below:
ALV files are available in sub folders:
After generating ALV files, users could go to Land -> Tools -> Create Land to create an internal land.
After creating a land, users could 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 has not been registered in the Land. Add sample metadata in Land Tab | Manage | Samples | Manage Sample Meta Data. If Manage Sample Meta Data is in grey (as in the screenshot below), you need to ask admin to change the land permissions for you.
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 Test Oncoland from above.
In the Manage Sample Meta Data page, users could click Add/Replace tab to add metadata table:
If use wants to link RNA-Seq bam files to data points in land view, the meta data table need a "BamFileName" column and the Land configuration needs a few BAM/BAS configuration options.
Explorer the land created
After uploading metadata, the land views would be available.
Create Virtual Land based on internal land and CCLE
To create a virtual land, go to Tools | Create Virtual Land". Note, the default server setting only allows administrators to be able to 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 one or multiple genes. The search includes data and samples from all Array Lands in this virtual land.
There is a column "Source Land" automatically added to the virtual land when it is created.