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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p><font face="Arial" size="2">Hi,</font>
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<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?
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<p><font face="Arial" size="2">Todd</font>
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<p><b><span lang="en-gb"><font color="#808080" face="Arial" size="1">Todd Moughamer</font></span></b>
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</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,
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