v30: custom gene tracks

All the gene tracks on the browser have been upgraded to a new format, and supported by a new mechanism. For all animal genomes all the gene track data have been updated with latest downloads from UCSC Genome Browser. A RefSeq genes and "xenoRefSeq genes" tracks are available for every animal genome and provides good annotation coverage, the latter provides homologous genes from other species.

This new gene track mechanism also supports custom gene tracks:

In above image two gene tracks are shown. The one on top is the native hg19 RefSeq gene track. The green track beneath it is an replica custom track. You can see from the details about this track in the menu box.

An example custom gene track can be found in this hg19 data hub, look for the word "hammock":

http://vizhub.wustl.edu/hubSample/hg19/hub.json


This page has some instructions about preparing gene tracks.

Download the browser source code from here or here.

v29 (4 of 4): the methylC track

Version 29 makes official unveil of the "methylC" track, though it has been available on our browser for a while.

The methylC track is able to display single-base DNA methylation data by discerning cytosine context (CG/CHG/CHH), strand-specificity, and incorporating confidence level data.

Thus it is excellent in visualizing whole-genome bisulfite sequencing (WGBS, or methylC-seq) results. In this case the confidence level data is read depth.

Surely it makes same support on Reduced Representation Bisulfite Sequencing (RRBS) results.

It can even be used for array-based methods such as Infinium 450K. In this case the -log10(P-value) will be used as confidence level.

Refer to http://epigenomegateway.wustl.edu/+/cmtk/ for more details.

A manuscript describing methylC track is under preparation.

v29 (3 of 4): delete custom tracks

We brought back a function that allows you to delete custom tracks in your current session.

After you've loaded custom tracks, click "CustomTK" > "List of all":

From the custom track listing you can find a "delete" button following each track. Click this button and the track will be gone, so be careful.