[maker-devel] Est2Genome Problems

[Christoph Hahn]

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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