New type=longTabix in development.

[Brian Lee]

The browser currently supports a new format called type=longTabix that can display inter-chromosomal interactions across the genome, here is an example custom track:

track type=longTabix name=longRange description="This data is using longTabix" bigDataUrl=http://hgwdev.cse.ucsc.edu/~braney/longRange/Esc_40kb_hindIII_rep1.over10.gz

Here is a session using this custom track: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.longTabix

Here is a mailing list archive describing the feature: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/kE2pIZUvfnA/jfopk7pFAQAJ

This longTabix track type points to a .gz file, where there is also a .gz.tbi file that provides an index.  The tab-separated .gz file has contents like the following (corresponding to the session area, please note that many of the example coordinates are about 40,000 bp apart: 14358129 14398129):

chr21 14358129 14398129 chr21:14678129-14718129,10.2666969602672 7864858 +

chr21 14598129 14638129 chr21:15118129-15158129,12.5964954534209 7864870 +

The .tbi file is built using the tabix software from: http://samtools.sourceforge.net/tabix.shtml 

Here is another session with a different example: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.other_regions

This gives an idea of what happens if there are coordinates to another chromosome, where in this session region there are data such as the following:

chr19 44116910 44119168 chr21:47876840-47878656,2 31515 .

This format may change with further development, feedback is welcomed.