[Gmod-help] Many Features

[todd.moughamer at syngenta.com]

Lincoln,
 
Thanks. Your solution seems like it would be much more digestible by the
end user especially at high coverage.
 
Best,
 
Todd

________________________________

From: lincoln.stein at gmail.com [mailto:lincoln.stein at gmail.com] On Behalf
Of Lincoln Stein
Sent: Monday, January 21, 2008 2:15 PM
To: Moughamer Todd USRE
Cc: help at gmod.org
Subject: Re: [Gmod-help] Many Features


Hi Todd,

The bumping algorithm will definitely die if you try to put too many
features into a single track. The algorithm could be made much more
efficient if we guarantee that names and descriptions won't be printed
on the features. 

What I'm doing in my own lab is not trying to show the overlapping
features directly, but instead to show a density plot of the number of
times a base pair was touched. I have plans to work on a glyph to
highlight SNPs and other variations, but I haven't started on it. 

Lincoln 


On Jan 21, 2008 1:59 PM, <todd.moughamer at syngenta.com> wrote:


	Hi, 

	I am attempting test Gbrowse's ability to render next gen
sequencing data...particularly short reads. I simulated thousands of
short overlapping 35 bp features over a 135 bp sequence. If I try to
render them on one track the best I can do is to set the number of
features cut off to 25...with the remaining features being condensed on
to one line. Increasing the cut off results in a timeout. Rendering data
on separate tracks would seem impractical since you would have to add a
line in the conf file for each. Any suggestions? 

	Todd 

	Todd Moughamer 

	Bioinformatics Consultancy & Training Group

	Syngenta Biotechnology, Inc.

	3054 Cornwallis Road, 1243.E

	Research Triangle Park, NC 27709-2257

	Tel: 919-597-3078

	Email: todd.moughamer at syngenta.com 
	www.syngenta.com 





-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20080121/8260385b/attachment.html>