[maker-devel] Maker quesiton

[Carson Holt]

Hi Jeff,

The structure of GFF3 files, means they cannot be concatenated. You can merge them by using the gff3_merge tool and giving it multiple GFF3 files (see usage statement).  It will take care of pulling them apart, reordering things, and then putting them back together in a usable way.

—Carson



> On Apr 28, 2015, at 5:58 PM, Jeff Maughan <jeff_maughan at byu.edu> wrote:
> 
> Hi!
> 
> I have a genome that is about 400 Mb.  I couldn’t get MPI to run on our server, so I just divided up the genome into 10Mb chucks and ran them separately.  Worked great (about 40 jobs).  I used fasta_merge and gff_merge on each of the subsets.  I thought I would then just concatenate (cat) each of the 40 files together and then I would be able to use maker_map_ids (etc.) and maker_functional_gff (etc) to rename and add function.  Unfortunately it seems to only map the ids for the first subset in the concatenated file…
> 
> Any ideas?  Is there another way to merge these files together so they play nice with the downstream scripts.
> 
> Thanks,
> 
> Jeff Maughan
> 
> PS I’m obviously not a trained bioinformaticist.
> 
> P. Jeff Maughan, Ph.D. | Professor | Department of Plant and Wildlife Sciences 
> 701 East University Parkway Drive
> 5144 LSB, Provo, Utah, 84602 | Brigham Young University
> http://lifesciences.byu.edu/~pjm43 <http://lifesciences.byu.edu/~pjm43>
> http://orphanedcrops.byu.edu/ <http://orphanedcrops.byu.edu/>
> *: Jeff_Maughan at byu.edu <mailto:Jeff_Maughan at byu.edu>
> (: (801) 422-8698
> 
> 
> 
> 
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