[maker-devel] Est2Genome Problems

[Carson Holt]

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> 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
> office: 517-884-7756
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