[maker-devel] Maker: Re-annotation

[Innocent Onsongo]

Maker Development Team, 

I am trying to use Maker for re-annotation using  gene predictions from Augustus. We had previously used Augustus for gene prediction but now want to combine these annotations with some EST data. I updated fields maker_opts.ctl  as below

genome=CGS01058.fasta #genome sequence file in fasta format

est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT

pred_gff=Augustus.gff3 #ab-initio predictions from

other_gff=Promoters.gff3 #promoter annotations

other_gff=CpG_Islands.gff3 # CpG island annotations

Maker runs to completion and according to the log file annotation was successful. However, it also gives a "Segmentation fault (core dumped)" message. It does produce a GFF3 file but when I load the GFF3 file into IGV and look it does not contain any of the exon definitions in Augustus.gff3. Am I missing something? 

Regards, 

Getiria

--
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532

[Carson Holt]

The option in trinity is --jaccard_clip

--> http://trinityrnaseq.sourceforge.net/#jaccard_clip

--Carson

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[Barry Moore]

Hi Getiria,

Does the MAKER produced GFF3 file contain any annotations at all?  Can you send the first ~100 lines each of the MAKER produced GFF3 file and of the GFF3 files that you passed via maker_opts.ctl?

B

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Barry Moore

Research Scientist

Dept. of Human Genetics

University of Utah

Salt Lake City, UT 84112

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[Innocent Onsongo]

One other thing, I ran MAKER with the RM_off flag (maker -f -RM_off -q) the input sequences had already been masked. 

   

On Wed, May 22, 2013 at 7:47 AM, Innocent Onsongo <onso...@umn.edu> wrote:

No. The MAKER produced GFF3 file does not contain any annotations. I even tried setting the keep_preds parameter to 1 (keep_preds=1) to see if it will pass annotations from the Augustus produced GFF file into the final annotation but that didn't work. I have attached the maker_opts.ctl file I used together with the first 100 lines of the GFF files it's using. I also include the GFF file produced by MAKER (CGS01058First100.gff)

[Carson Holt]

Are you using MAKER version 2.10? I ask because there is in issue with other_gff in that version that has since been fixed.  So if you don't get other_gff to pass-through, you will need to upgrade to 2.28 (release date is later today coincidentally).

For the Augustus GFF3 file, the format is a little weird which is causing the problem.  They are mRNA features not attached to genes.  Rather than build the expected 3 level gene/mRNA/exon structure for these, it is simpler just to convert it to the 2 level match/match_part structure.  Just convert the 'mRNA' tag to 'match' and all 'exon' tags to 'match_part'.  Rename the GFF3 when your done so that it will force rebuild of the GFF3 database when you run again.

Thanks,

Carson

[Innocent Onsongo]

No. The MAKER produced GFF3 file does not contain any annotations. I even tried setting the keep_preds parameter to 1 (keep_preds=1) to see if it will pass annotations from the Augustus produced GFF file into the final annotation but that didn't work. I have attached the maker_opts.ctl file I used together with the first 100 lines of the GFF files it's using. I also include the GFF file produced by MAKER (CGS01058First100.gff)

On Tue, May 21, 2013 at 10:43 PM, Barry Moore <barry...@gmail.com> wrote:

[Innocent Onsongo]

I upgraded to 2.28 and Maker is not running. Thanks!

[Carson Holt]

What does it do?

--Carson

[Innocent Onsongo]

Oops! I meant to type Maker is NOW running.