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<div class="moz-cite-prefix">Dear Carson,<br>
<br>
Thanks for getting in touch! I actually managed in the end. I
converted the gtf I had from cufflinks to gff3 via the script
'gtf2gff.pl' from augustus and then used the script
'gffGetmRNA.pl' again from augustus to extract the mRNA in fasta.
This file I fed to MAKER via the 'est=' route and now I get plenty
of est2genome evidence in the maker result. So the problem seems
to be limited to the route 'est_gff=', allthough there is no error
message whatsoever the est2genome routine seems to never be
triggered. <br>
<br>
I'd still be happy to upload my data (the cufflinks gff, the
genome fasta, anything else?) if you want to try to reproduce the
problem. Let me know!<br>
<br>
btw I seem to be unable to create a new topic or respond to topics
via google groups. Is the list closed or the access restricted
somehow. I only managed by responding to Jason's mail which I
still had in my inbox directly via my gmail.<br>
<br>
Thanks!<br>
<br>
cheers,<br>
Christoph<br>
<br>
On 09/03/2017 19:39, Carson Holt wrote:<br>
</div>
<blockquote
cite="mid:33720C49-5D1B-46DF-A89C-43A7683D7C02@gmail.com"
type="cite">
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<div class="">Jason never responded back to this one or uploaded
his file to test. He probably figured it out off list. My guess
is that your results are too fragmented to build a model that
can pass filtering thresholds with.</div>
<div class=""><br class="">
</div>
<div class="">If you want I can take a look. You can upload all
files for a test job here —> <a moz-do-not-send="true"
href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi"
class="">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div>
<div class=""><br class="">
</div>
<div class="">—Carson</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Mar 7, 2017, at 5:51 PM, Christoph Hahn <<a
moz-do-not-send="true"
href="mailto:chrisi.hahni@gmail.com" class="">chrisi.hahni@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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http-equiv="Content-Type" class="">
<div bgcolor="#FFFFFF" text="#000000" class="">
<div class="moz-cite-prefix">Hi MAKER community,<br
class="">
<br class="">
I think I am seeing the same issue that Jason has
reported. ran cufflinks, then cufflinks2gff3 and tried
to feed the result to MAKER via 'est_gff=' with
'est2genome=1'. In the resulting gff file from maker I
only get protein2genome and repeatmasker evidence. If I
do a search in the maker log est2genome never comes up.
Tried to extract the cufflinks results as fasta and feed
to MAKER via 'est='. Still no indication that the
evidence is used.<br class="">
<br class="">
I am using MAKER 2.31.8. Any help would be much
appreciated! Thanks in advance for your time!<br
class="">
<br class="">
cheers,<br class="">
Christoph<br class="">
<br class="">
On 10/02/2015 17:56, Carson Holt wrote:<br class="">
</div>
<blockquote
cite="mid:119684F8-8071-4318-A129-3D90EC54242A@gmail.com"
type="cite" class="">
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charset=utf-8" class="">
<div class="">I ran a few est2genome runs with a
cufflinks file i just generated and did not get any
issues for EST based gene models.</div>
<div class=""><br class="">
</div>
<div class="">I’d like to at least have your test set to
see if I can duplicate what you are seeing.</div>
<div class=""><br class="">
</div>
<div class="">Use this to upload the job files then I
can just run it from my server here —> <a
moz-do-not-send="true"
href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi"
class="">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div>
<div class=""><br class="">
</div>
<div class="">—Carson</div>
<div class=""><br class="">
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Feb 3, 2015, at 11:13 AM, Jason
Gallant <<a moz-do-not-send="true"
href="mailto:jgallant@msu.edu" class="">jgallant@msu.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class=""> <span id="mailbox-conversation"
class="">
<div class="">Hi Folks,</div>
<div class=""><br class="">
</div>
<div class="">I’ve nearly succeeded at getting
MAKER to run on AWS— I’ve been checking the
output files, and have noticed that none of
my RNAseq data was incorporated on the run.
I used Cufflinks to perform alignments of
libraries from several tissues, ran the
accessory script cufflinks2gff3 for each
tissue, then concatenated the resulting gff3
files. I even ran the accessory script
gff3merge to check that the resulting file
was properly formatted.</div>
<div class=""><br class="">
</div>
<div class="">For options, I set est2genome=1
and est_gff=cufflinks.gff. I only get
protein2genome and repeatmasker evidence in
my resulting maker gff3 file, and the genes
predicted by these. Is there another option
that I need to enable in order to use my
est_gff file? I’m trying to get a set of
genes to train the predictors for my next
step.</div>
<div class=""><br class="">
</div>
<div class="">Any help would (as always) be
greatly appreciated!</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Jason Gallant</div>
</span>
<div class="mailbox_signature"> <br class="">
—<br class="">
Dr. Jason R. Gallant
<div class="">Assistant Professor</div>
<div class="">Room 38 Natural Sciences<br
class="">
<div class="">Department of Zoology</div>
<div class="">Michigan State University</div>
<div class="">East Lansing, MI 48824</div>
<div class=""><a moz-do-not-send="true"
href="mailto:jgallant@msu.edu" class="">jgallant@msu.edu</a></div>
</div>
<div class="">office: 517-884-7756</div>
</div>
</div>
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