<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi MAKER community,<br>
<br>
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>
<br>
I am using MAKER 2.31.8. Any help would be much appreciated!
Thanks in advance for your time!<br>
<br>
cheers,<br>
Christoph<br>
<br>
On 10/02/2015 17:56, Carson Holt wrote:<br>
</div>
<blockquote
cite="mid:119684F8-8071-4318-A129-3D90EC54242A@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<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>
<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>
_______________________________________________<br class="">
maker-devel mailing list<br class="">
<a moz-do-not-send="true"
href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br
class="">
<a class="moz-txt-link-freetext" href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
maker-devel mailing list
<a class="moz-txt-link-abbreviated" href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a class="moz-txt-link-freetext" href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</pre>
</blockquote>
<p><br>
</p>
</body>
</html>