<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=us-ascii">
<META content="MSHTML 6.00.2800.1605" name=GENERATOR></HEAD>
<BODY>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2>Lincoln,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2>Thanks. Your solution seems like it would be much more
digestible by the end user especially at high coverage.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2>Best,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=302282619-21012008><FONT face=Arial
color=#0000ff size=2>Todd</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> lincoln.stein@gmail.com
[mailto:lincoln.stein@gmail.com] <B>On Behalf Of </B>Lincoln
Stein<BR><B>Sent:</B> Monday, January 21, 2008 2:15 PM<BR><B>To:</B> Moughamer
Todd USRE<BR><B>Cc:</B> help@gmod.org<BR><B>Subject:</B> Re: [Gmod-help] Many
Features<BR></FONT><BR></DIV>
<DIV></DIV>Hi Todd,<BR><BR>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. <BR><BR>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. <BR><BR>Lincoln <BR><BR>
<DIV class=gmail_quote>On Jan 21, 2008 1:59 PM, <<A
href="mailto:todd.moughamer@syngenta.com">todd.moughamer@syngenta.com</A>>
wrote:<BR>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<DIV>
<P><FONT face=Arial size=2>Hi,</FONT> </P>
<P><FONT face=Arial size=2>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? </FONT></P>
<P><FONT face=Arial size=2>Todd</FONT> </P>
<P><B><SPAN lang=en-gb><FONT face=Arial color=#808080 size=1>Todd
Moughamer</FONT></SPAN></B> </P>
<P align=justify><SPAN lang=en-gb><FONT face=Arial color=#808080
size=1>Bioinformatics Consultancy & Training Group</FONT></SPAN></P>
<P align=justify><SPAN lang=en-gb><FONT face=Arial color=#808080
size=1>Syngenta Biotechnology, Inc.</FONT></SPAN></P>
<P align=justify><SPAN lang=en-gb><FONT face=Arial color=#808080 size=1>3054
Cornwallis Road, 1243.E</FONT></SPAN></P>
<P align=justify><SPAN lang=en-gb><FONT face=Arial color=#808080
size=1>Research Triangle Park, NC 27709-2257</FONT></SPAN></P>
<P align=justify><SPAN lang=en-gb><FONT face=Arial color=#808080 size=1>Tel:
919-597-3078</FONT></SPAN></P>
<P><SPAN lang=en-gb><FONT face=Arial color=#808080 size=1>Email: <A
href="mailto:todd.moughamer@syngenta.com"
target=_blank>todd.moughamer@syngenta.com</A></FONT></SPAN> <BR><SPAN
lang=en-gb><U></U></SPAN><A><SPAN lang=en-gb><U><FONT face=Arial color=#0000ff
size=1>www.syngenta.com</FONT></U><U></U></SPAN></A><SPAN
lang=en-gb><U></U></SPAN><SPAN lang=en-us></SPAN>
</P><BR></DIV></BLOCKQUOTE></DIV><BR><BR clear=all><BR>-- <BR>Lincoln D.
Stein<BR>Cold Spring Harbor Laboratory<BR>1 Bungtown Road<BR>Cold Spring Harbor,
NY 11724<BR>(516) 367-8380 (voice)<BR>(516) 367-8389 (fax)<BR>FOR URGENT
MESSAGES & SCHEDULING, <BR>PLEASE CONTACT MY ASSISTANT, <BR>SANDRA
MICHELSEN, AT <A href="mailto:michelse@cshl.edu">michelse@cshl.edu</A>
</BODY></HTML>