[maker-devel] running MAKER to merge annotations

[Daniel Ence]

Hi Arun, are the three rounds of maker on different parts/versions of the genome or did you maker on the same genome with three different settings? If it’s the former, then you can merge the maker gff files with gff3_merge, which is included with your maker installation. 

If it’s the latter case then I do think EVM could help if you want to give the different result sets different confidence weights. If you want to give them all the same weight, then you could do another run of maker, and pass them through as either models or predictions.

~Daniel





Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Jan 1, 2016, at 11:31 AM, Arun Seetharam <arnstrm at gmail.com> wrote:
> 
> Hi all,
> 
> First of all, a very happy new year to all of you! I hope everyone is having a great holiday season.
> 
> I have a question about Maker. For my grass species, I ran 3 separate rounds of MAKER (low GC, regular GC and high GC) and I now have 3 maker gff files. So, what is the correct way to merge these files to a single gff file? Do I have to run a maker round with just the GFF files as input? It looks like EVM especially meant to do this kind of job, but not sure if Maker does this too.
> 
> Thanks for any help or suggestions!
> 
> Have a nice day,
> -- 
> Arun Seetharam
> Post Doctoral Research Associate
> Genome Informatics Facility & EEOB
> Office of Biotechnology
> 228 Science I
> Iowa State University
> Ames, Iowa 50011
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