<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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 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 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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<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="">
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<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>
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</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="">
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<br class="">
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<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>
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<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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