Sunday, September 23, 2012

v10 minor update: bug fix and more scrolling options

Download source code from dropbox.

This code release fixed a bug associated with SAM track display. When displaying read alignment data during genomic juxtaposition mode, the track image appeared to be shifted due to the bug, now it's fixed.

Besides, you can now drag on any of the genome annotation tracks to scroll.

Try this link to open the browser and show the tracks as displayed in the screen shot below:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=LTR&gftk=LTR,full&coordinate=chr1:1340000-1390000&custombam=stat1hela,http://vizhub.wustl.edu/hubSample/hg19/sam1.gz,thin


As illustrated in this example, genomic juxtaposition focuses the view on LTR elements and reveals that STAT1 ChIP-Seq reads bind one LTR copy, suggesting this LTR copy has something to do with STAT1's business in HeLa cells.

STAT1 ChIP-Seq data comes from this publication: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing