Sunday, September 9, 2012

v8 major update - tabix indexing, chromHMM tracks

The WashU Genome Browser has been on a fast track of change. Today we announce yet another major update.


tabix for file indexing/querying
The Browser is now using tabix to store, index and query the track files (http://samtools.sourceforge.net/tabix.shtml).

Tabix is a peer of UCSC's bigWig/bigBed system, except it is much more generic and simpler.

Users using the custom tracks need to migrate their data. Please refer to following posts on how to convert UCSC formats to tabix format:

bigWig to tabix
bigBed to tabix
BAM to tabix




chromatin state tracks (categorical data)

Broad chromatin state data (http://compbio.mit.edu/ChromHMM/) on 9 human cell lines are now displayed. Data is obtained from ENCODE project. To see all of them, click the link below:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&hmtk=wgEncodeBroadHmmGm12878HMM,wgEncodeBroadHmmH1hescHMM,wgEncodeBroadHmmHepg2HMM,wgEncodeBroadHmmHmecHMM,wgEncodeBroadHmmHsmmHMM,wgEncodeBroadHmmHuvecHMM,wgEncodeBroadHmmK562HMM,wgEncodeBroadHmmNhekHMM,wgEncodeBroadHmmNhlfHMM&metadata=Sample


The chromHMM tracks are underlain by a new type of track -- the track with categorical data. This type of tracks are displayed in genome heatmap along all the genome-wide quantitative assay results, but show data of categorical nature, e.g. different chromatin states.


When you invoke the configuration options on the chromatin state tracks, you will see quite different options compared with quantitative tracks. That is, the complete list of "states" or "categories", and controls to change the color of each state.

This new feature is still under development. We're working to make the custom track support on this new track type.