Friday, March 14, 2014

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.