[maker-devel] Est2Genome Problems

[Carson Holt]

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> 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 <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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