Ok, I updated to the newest version of gbowse (the new version is at:<br><a href="http://vm-gmod.eecs.wsu.edu/cgi-bin/gb2/gbrowse/primer2/?start=253;stop=352;ref=genome;width=800;version=100;flip=0;grid=1;id=1ae82ac1261f191c48bd51641c91191a;label=DNA-Primer">http://vm-gmod.eecs.wsu.edu/cgi-bin/gb2/gbrowse/primer2/?start=253;stop=352;ref=genome;width=800;version=100;flip=0;grid=1;id=1ae82ac1261f191c48bd51641c91191a;label=DNA-Primer</a>)<br>
<br>As you can see I am still seeing the same glyph problem.<br><br><div class="gmail_quote">On Mon, Apr 26, 2010 at 1:45 PM, Artemus Harper <span dir="ltr"><<a href="mailto:subanark@gmail.com">subanark@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">I do have an old version of Gbrowse (not sure how to determine my current version), I'm trying to update it right now, but I'm running into some issues. The install script says it cannot find CBuilder.pm, which I assume may be included in a newer version of perl I have installed (5.8.8) which according to the wiki is high enough to install with. I'll get perl updated once I resolve my conflict with the repos.<div>
<div></div><div class="h5"><br>
<br><div class="gmail_quote">On Mon, Apr 26, 2010 at 12:49 PM, Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:help@gmod.org" target="_blank">help@gmod.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi Artemus,<div><br></div><div>I think you've found a bug. The primers appear to only be correctly aligned when the view includes the start point for the primer. The code is also showing too much DNA for the primers, making the primer DNA image be too wide.</div>
<div><br></div><div>Does anyone have an idea on this, other than a coding bug?</div><div><br></div><div>Thanks,</div><div><br></div><div>Dave C.</div><div><br></div><div> <br><br><div class="gmail_quote"><div><div></div>
<div>On Fri, Apr 23, 2010 at 11:09 AM, Artemus Harper <span dir="ltr"><<a href="mailto:subanark@gmail.com" target="_blank">subanark@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>I'm trying to use the glyph dna to see nucleotide sequences when you zoom in. However, this doesn't seem to be working for features. In particular, if a contig refers to a part of another contig, it isn't displaying the right data when the start of the sequence is not in view.<br>
<br>For example, I'm looking at one of my sequences starting at genome:470.570. I see:<br><br><-----------------------------------------------<br>470<br>DNA/GC Content<br>tgtgatttctatgttatgta...<br><br>Primers<br>
S4<br>
gatttctatgttatgta...<br><br>But when I move over to the right:<br><-----------------------------------------------<br>
500<br>DNA/GC Content<br>
taagggcatatcggttgaag...<br>
<br>
Primers<br>S4<br> cgaagaaacaaattatattt...<br clear="all"><br>which for S4 isn't what was displayed at 500, although it is for the genome sequence.<br><br>You can see this yourself (when the two tracks are turned on):<br>
<a href="http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:470..570" target="_blank">http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:470..570</a><br>and when shifted over:<br><a href="http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:500..600" target="_blank">http://gmod.eecs.wsu.edu/cgi-bin/gbrowse/primer2/?name=genome:500..600</a><br>
-- <br><font color="#888888">Artemus Harper<br>
</font><br></div></div>------------------------------------------------------------------------------<br>
<br>_______________________________________________<br>
Gmod-gbrowse mailing list<br>
<a href="mailto:Gmod-gbrowse@lists.sourceforge.net" target="_blank">Gmod-gbrowse@lists.sourceforge.net</a><br>
<a href="https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse" target="_blank">https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse</a><br>
<br></blockquote></div><br><br clear="all"><br>-- <br>===> PLEASE KEEP RESPONSES ON THE LIST <===<br><a href="http://gmod.org/wiki/GMOD_Logo_Program" target="_blank">http://gmod.org/wiki/GMOD_Logo_Program</a><br><a href="http://gmod.org/wiki/GMOD_News" target="_blank">http://gmod.org/wiki/GMOD_News</a><br>
Was this helpful? <a href="http://gmod.org/wiki/Help_Desk_Feedback" target="_blank">http://gmod.org/wiki/Help_Desk_Feedback</a><br><br>
</div>
</blockquote></div><br><br clear="all"><br></div></div>-- <br><font color="#888888">Artemus Harper<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Artemus Harper<br>