v27 (3 of 3): custom track listing

We brought back a missing feature, which allows you to view the entire list of custom tracks that have been loaded.

Click "CustomTK" button and find the "List of all" option. You need to load a datahub or some custom tracks first or these options won't show up:

Click this option to see a listing of all your custom tracks:

Those ones that are already on display are shown as inactive labels. Click the active ones and select a bunch to display on the browser.

Such track listing function is necessary as it allows you to find tracks that are NOT ANNOTATED by any metadata terms.

Those annotated by metadata terms will show up in the facet table, as described in this post: v24 (3 of 3): facet panel

v27 (2 of 3): make screenshot for Genome snapshot

The Genome snapshot (used to be call "bird's eye view") is often found useful. It is now made more useful with the SVG output.

Simply click the "screenshot" button on top of the panel to do it. A few seconds later a link will appear right next to the button showing you the SVG file.

v27 (1 of 3): GENCODE V17 track for the human genome

GENCODE version 17 of the human genes are now on hg19. Credit goes to UCSC Genome Browser where the data was obtained. GENCODE is one of the most finely curated gene tracks out there, and we're really happy to have it in our Browser.

http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gencodeV17,full

Genes are assigned into 5 categories, distinguished by color:

      coding genes
      non-coding genes
      pseudogenes
      with problem!
      polyA signal

For the "problem" ones, their causes can be seen in the tooltip bubble, such as "retained_intron".

In the tooltip, links are given to the gene model's record in GENCODE database.



This is the start of the effort to improve all the gene tracks on our Browser, including the underlying mechanism. Right now the GENCODE V17 track is new format and is supported by new mechanism, alongside the old gene tracks such as refGene, GENCODE V11.

With the new mechanism we can reduce the dependence on mysql storage and store all the data in the compressed track file, so that the new gene tracks can work as custom tracks. On such basis a new track type is been developed to support the RNA-seq experiments.