[maker-devel] Est2Genome Problems

Fri Mar 10 01:50:52 MST 2017

Dear Carson,

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.

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!

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.

Thanks!

cheers,
Christoph

On 09/03/2017 19:39, Carson Holt wrote:
> 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.
>
> If you want I can take a look. You can upload all files for a test job 
> here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>
> —Carson
>
>
>
>> On Mar 7, 2017, at 5:51 PM, Christoph Hahn <chrisi.hahni at gmail.com 
>> <mailto:chrisi.hahni at gmail.com>> wrote:
>>
>> Hi MAKER community,
>>
>> 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.
>>
>> I am using MAKER 2.31.8. Any help would be much appreciated! Thanks 
>> in advance for your time!
>>
>> cheers,
>> Christoph
>>
>> On 10/02/2015 17:56, Carson Holt wrote:
>>> I ran a few est2genome runs with a cufflinks file i just generated 
>>> and did not get any issues for EST based gene models.
>>>
>>> I’d like to at least have your test set to see if I can duplicate 
>>> what you are seeing.
>>>
>>> Use this to upload the job files then I can just run it from my 
>>> server here —> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi
>>>
>>> —Carson
>>>
>>>
>>>> On Feb 3, 2015, at 11:13 AM, Jason Gallant <jgallant at msu.edu 
>>>> <mailto:jgallant at msu.edu>> wrote:
>>>>
>>>> Hi Folks,
>>>>
>>>> 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.
>>>>
>>>> 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.
>>>>
>>>> Any help would (as always) be greatly appreciated!
>>>>
>>>> Best,
>>>> Jason Gallant
>>>>
>>>> —
>>>> Dr. Jason R. Gallant
>>>> Assistant Professor
>>>> Room 38 Natural Sciences
>>>> Department of Zoology
>>>> Michigan State University
>>>> East Lansing, MI 48824
>>>> jgallant at msu.edu <mailto:jgallant at msu.edu>
>>>> office: 517-884-7756
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>>>
>>>
>>>
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