[DAS] Stylesheets and contigview

[Simon Twigger]

Hi there,

Taking my first personal foray into DAS, have the LDAS server working  
very nicely (Mac OS X 10.2) and I've been playing around with some rat  
annotations viewed on the Ensembl contigview. I tried setting a style  
sheet as described in the LDAS installation manual (which was great,  
very easy to follow) and it doesnt seem to be having any effect on how  
things appear on the contigview display.

Sample .das annotations:

[annotations]
SSLP	D2Rat239	microsatellite	epcr	1	16662	16847	.	.	.
SSLP	D2Rat381	microsatellite	epcr	1	72253	72498	.	.	.
SSLP	D1Rat245	microsatellite	epcr	1	1571523	1571694	.	.	.

Style sheet:

[microsatellite]
glyph		= primers
bgcolor		= black
fgcolor		= red
height		= 6
bump		= 1

Ignoring the fact that microsatellites thought to be on Chr2 are  
appearing on chromosome 1 when we run ePCR, will this combination of  
annotation and style sheet work to give me the primer glyph on  
contigview? Everything displays as a box glyph (I presume this is the  
default) and the color seems to be whatever I set in the 'Manage  
Sources' options on the contigview.

I noticed that the description of style sheets in the LDAS page is very  
GBrowse-like whereas the official stylesheet documentation  
(http://www.biodas.org/documents/spec.html) referred to on the LDAS  
page is full blown XML - do both of these work, should I use one rather  
than the other?

Any advice would be most appreciated.

Cheers,

	Simon.


------------------------------------------------------------------------ 
--------------------------
Simon Twigger, Ph.D.
Assistant Professor, Bioinformatics Research Center

Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, 53226
tel. 414-456-8802, fax 414-456-6595