Friday, May 31, 2013

v18: new page look, BAM file support

Version 18 code release features a lot of improvements, including new look of user interface throughout the entire browser, and most importantly, the support of BAM files.

You can get the source code from dropbox, or from our web site.

BAM file support

Open up the browser and click "CustomTk" button in the toolbox to show this:

Click button "BAM" to and we're ready to submit a custom BAM track:

Enter URL and track name, and press  . Following shows the display of sample BAM track of human hg19 genome:

Clicking on a read will invoke a bubble showing detailed info about the read, including its alignment:

Showing a paired-end sequencing assay result, where reads mapped on forward strand are in  teal , and reads on reverse strand are in  fuchsia . Mismatches are in  yellow . Clipped bases are in  gray .

Details about mismatches, insertion, deletion, clipping can also be viewed in the bubble. For instance:

A BAM track can also be submitted via URL parameter, and also through data hub.

For instance, the following URL displays a BAM file in hg19 genome:,,thin

Finally, the SAM files are no longer supported.

Credit: Chee-Hong Wong

New user interface