Genomic juxtaposition

This type of view is similar as Gene Set View, but instead of displaying data for a short list of genes/items, it re-arrange the view according to positional data in a genomic feature track. Following diagram indicates how juxtaposition works:

This function can be used to show data from a genomic feature track contains tens of thousands of genomic features, while Gene Set View yields optimum performance with less than 500 items.

But unlike Gene Set View, the order of appearance of genomic features cannot be rearranged in genomic juxtaposition.

At control panel, go to "Genomic view" → "Genomic juxtaposing" to find the interface:

We need to select a genomic feature track in order to run juxtaposition. Click the "select track" button:

The genomic feature track selection panel pops out. Here we select the track "UCSC genes". After a short while, the Browser finishes computing and goes into Genomic Juxtaposition mode. The control panel will look like:

In the genome heatmap, data are displayed over genes, with gray lines in between. In the genomic feature track (which in this case it is UCSC genes track), alternating background color is used to indicate gene segments:

More convenient way to run Genomic Juxtaposition is to turn on the genomic feature track of interest, right click on this track image, and select "juxtaposition" option in the menu:

The juxtaposition can also be applied to custom bigBed tracks.


Last modifed: 1/2/2012