v35: hammock tracks for richly annotated genomic features

The hammock tracks is a new track type for displaying richly annotated genomic feature on the browser. It's simple and straight, succinct by having only 4 columns, versatile for the JSON field, and can do awesome things. The current format specification is here:

http://wiki.wubrowse.org/Hammock


The format is under active development, and suggestions are always welcome. It will also remain backward-compatible by its JSON nature.

bgzip and tabix should be used to compress and index a hammock file for browser display, same as the bedGraph track.

Usually you need to submit a hammock track via a JSON datahub, as can be seen in this example:  http://vizhub.wustl.edu/hubSample/hg19/hub.experiment

Show this example.




A few screenshots:


Gencode track. Featuring the structure display for gene models, and color assignments for different types of genes (coding/non-coding/pseudo...):



Two classes of repeat features displayed in one track (SINE and DNA). Degree of darkness is determined by the Swiss-Waterman score of each feature (with regard to max score of all features in the view range):







The same repeat track as above, displayed in "barplot" mode, showing the Smith-Waterman scores displayed as bars on top of repeat features. Bar width is the same as the on-screen width of that item, and bar color is similar but slightly lighter than the item color:




Another barplot example showing exon array data. featuring the overlapping display of bars (for items that overlap with each other):





 NarrowPeak data display, with the tooltip showing detailed information on the clicked item:

v34 (2 of 2): convenient coordinate choices

A minor improvement is introduced to the browser on version 34, that allows coordinates to be entered into browser conveniently in several commonly used forms, as described below:


Single base pair on a chromosome

http://epigenomegateway.wustl.edu/browser/?genome=hg18&datahub_jsonfile=http://vizhub.wustl.edu/public/hg18/pmid19829295/hub&coordinate=chr1:5932545

This URL contains the "coordinate" parameter which takes the browser to the given location. The coordinate is chr1:5932545, which is a single base pair. The browser displays a region with this basepair in the middle and shows at highest resolution possible:

The browser also highlights the given base pair with yellow triangle shape on the coordinate ruler on top of the tracks.

At any time, you can also enter the coordinate string in the form of "chrX 12345" into the coordinate box and jump to it, as demonstrated below:


Single base pair in current chromosome

While you're looking at a specific chromosome using the browser, you can quick change to the position of a specific base pair in this chromosome. Click the navigation button on top of the browser and enter the coordinate of that base pair (just digits, no chromosome name) and press Enter:

And it shows up:

This is same effect of entering "chr1:17836214", but since the browser was showing chromosome 1, you can skip "chr1" from the coordinate string.


1,234,567

Some folks prefer to see large numbers in this way. Now that is also allowed by the browser to input coordinates.