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Hi Scott and Josh<br>
<br>
I tried mRNA:CG11372.a and that doesn't work either (you can try for
yourself at <a class="moz-txt-link-freetext" href="http://mblab.wustl.edu/cgi-bin/gbrowse/fly5">http://mblab.wustl.edu/cgi-bin/gbrowse/fly5</a>).<br>
I did add mRNA to the automatic classes, but that doesn't help.<br>
<br>
CG11372.a is a correct ID in MB5, the track I that's shown on this
browser. The corresponding FlyBase gene is CG11372-RA. <br>
<br>
-Jeltje<br>
<br>
<br>
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<blockquote type="cite">
<pre wrap="">Hi Jeltje,
Can you try searching for mRNA:CG11372.a and see if that works? If
so, you just need to add mRNA to your automatic classes line in the
conf file.
Scott</pre>
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<br>
Josh Goodman wrote:
<blockquote cite="mid48C93E2B.2040506@indiana.edu" type="cite">
<pre wrap="">Hi Dave,
Can you tell me what you were searching for because I don't see this problem on FlyBase? Using an
ID, Name, or Alias turns up the correct hit as far as I can tell. If you were using 'CG11372.a'
then that is expected because that isn't a valid FlyBase ID, symbol, or synonym.
Thanks,
Josh
Dave Clements, GMOD Help Desk wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Jeltje,
I don't see any problem with your configuration or the data file, and
I have the same interpretation of the tutorial as you do.
Which means, um, that I don't have any idea what is wrong.
I can tell you that the GBrowse installation at FlyBase appears to
have the same problem. You can't search on mRNA names there either.
I suspect that this is a GBrowse problem rather than a configuration
or data problem.
Does anyone else have any insight on this?
Thanks,
Dave C.
GMOD Help Desk
On Wed, Sep 10, 2008 at 11:08 PM, Jeltje van Baren <a class="moz-txt-link-rfc2396E" href="mailto:jeltje@wustl.edu"><jeltje@wustl.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hey all
According to the tutorial, anything that has a Name or Alias attribute in
the GFF3 file can be searched for by name. However, this is not the behavior
I see.
I can search by gene name, but not my mRNA ID or Name.
This is a sample of my GFF3:
2L MBannot5 gene 72388 76206 0 + .
ID=CG11372;Name=CG11372
2L MBannot5 mRNA 72388 76203 1 + .
ID=CG11372.a;Parent=CG11372;Name=CG11372.a
2L MBannot5 exon 72388 72977 1 + .
Parent=CG11372.a
2L MBannot5 exon 74903 75018 1 + .
Parent=CG11372.a
2L MBannot5 exon 75078 76203 1 + .
Parent=CG11372.a
2L MBannot5 five_prime_UTR 72388 72602 1 +
0 Parent=CG11372.a
2L MBannot5 start_codon 72603 72605 1 +
0 Parent=CG11372.a
2L MBannot5 CDS 72603 72977 1 + 0
Parent=CG11372.a
2L MBannot5 CDS 74903 75018 1 + 0
Parent=CG11372.a
2L MBannot5 CDS 75078 76098 1 + 1
Parent=CG11372.a
2L MBannot5 stop_codon 76096 76098 1 +
0 Parent=CG11372.a
2L MBannot5 three_prime_UTR 76099 76203 1 +
0 Parent=CG11372.a
I can type CG11372 in the Search box, and then all transcripts are
highlighted. Searching for CG11372.a results in a "The landmark named
CG9171.a is not recognized." message.
I tried prefixing with the Source name (MBannot5) and the Track ID (MB5),
like so: MB5:CG9171.a (I seem to remember one of these used to be possible)
but that doesn't work.
I also tried adding ID and Name to 'search attributes' in the config file,
but to no avail.
I'm running the stable 1.69 version.
You can find the gbrowser at
<a class="moz-txt-link-freetext" href="http://mblab.wustl.edu/cgi-bin/gbrowse/fly5/">http://mblab.wustl.edu/cgi-bin/gbrowse/fly5/</a>
and the config file at
<a class="moz-txt-link-freetext" href="http://mblab.wustl.edu/~jeltje/fly5.conf">http://mblab.wustl.edu/~jeltje/fly5.conf</a>
What am I missing?
-Jeltje
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</pre>
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<pre wrap="">
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