[maker-devel] Why are some start positions minus in the gff result?

[Carson Holt]

I'm thinking the same thing.  Reviewing how I parse GeneMarks output, I just
use their start and end coordinates (no changes).  Over the weekend I
altered the GeneMark parser to walk the gene start away from the supposed
origin so as not to let this happen.  In your E. coli test case since you
have multiple contigs for what is likely a single circular genome, this
would be the correct behavior as you don't want to treat each contig as an
independent circular chromosome.  I should probably add an is_circular
option to the control files so users can select for this. I've updated the
maker subversion repository so you can do an 'svn update' (I believe you are
using the devel version of MAEKR correct?)

Thanks,
Carson



From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Monday, 1 April, 2013 12:27 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Why are some start positions minus in the gff
result?

Hi, I seem to remember some discussion of the possibility of negative
coordinates in a gff3 file when the genomic material is circular. Since
you're annotating viral genomes, could this be whats happening here? Like
Carson said, I've never seen this before, but that's just an idea I had.

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

From: maker-devel-bounces at yandell-lab.org
[maker-devel-bounces at yandell-lab.org] on behalf of Hung-Wei Hsu
[ares711122 at gmail.com]
Sent: Monday, March 25, 2013 8:50 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] Why are some start positions minus in the gff result?

Hi MAKER developers,

I could successfully run MAKER and get the final gff.
But I found some start positions in the gff were minus.
That led to error in the gff reader.
Is this a bug?
Could you please help to resolve this problem?
Thanks a lot in advance.

Best regards,
Hung-Wei
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