Saturday, March 22, 2014

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:

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:

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: