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After searching for an gene, users can get this view by clicking View -> RNA-Seq Quantification -> Genome Browser (Exon Details).

LandExonJunction 1.png

The view is organized by tumor type by default. This can be changed by using the right panel Task -> Specify group Column. Choose "Sample Type" if want to compare tumor sample with normal samples.

Right click on any alignment track to select Set Track Properties.

LandExonJunction 2.png

Select all the alignment tracks from let panel and change the option Show Exon Junction to Always.

LandExonJunction 3.png

Browse the data and determine the junction of interest for further visualization and analysis. The Junction ID can be get by moving mouse over the junction

LandExonJunction 5.png

Users can focus only on this junction by filtering the Junction ID

LandExonJunction 4.png

Change the group column to Sample ID to show exon junction for individual samples.

LandExonJunction 10.png

Again, right click on any alignment track to "Set Track Properties". To allow all exon junctions to show, set the Minimal Count to 1 and set Show Exon Junction to Always.

LandExonJunction 11.png

To view the detailed sample information for this junction, group sample set from the filter.

LandExonJunction 6.png

LandExonJunction 7.png

then download the GeneBas data as Matrix (for all genes) to local analysis, so that it is very easy to filter by sample meta data and junction annotation. More details about downloading function DownloadLandData_AllGenes.pdf.

LandExonJunction 8.png

Load the previous sample set.

LandExonJunction 9.png

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