[maker-devel] question about Maker2

[Carson Holt]

Hi Giancarlo,

Anything listed as something like maker-*-augustus was a result of MAKER sending hints to augustus, and anything like augustus-*-abinit was the result of augustus run directly from the HMM without hints.

Here is more detail on the format —>
<top_level_source> - <contig> - <internal_source> -gene- <chunk> - <iterator>

Top level possibilities:
maker                      #maker generated model
snap_masked          #snap run on masked sequence
augustus_masked   #augustus run on masked sequence
etc.

Internal source:
abinit        #ab initio model direct from HMM
snap         #hints provided to SNAP (alters scoring)
augustus  #hints provided to augustus (alters scoring)

Then chunk and iterator are just to generate a uniq ID.


Example:
augustus_masked-scaffold11899-abinit-gene-0.6    #Produced by Augustus on masked sequence using raw HMM (no MAKER intervention).
maker-scaffold11899-augustus-gene-0.6                 #Produced by maker sending hints to augustus to modify scoring against the HMM

—Carson



> On 3/24/16, 9:23 AM, "giancarlo.russo" <giancarlo.russo at fgcz.ethz.ch>
> wrote:
> 
>> Dear Mike,
>> 
>> first of all thanks for taking care and sharing Maker, as part of the
>> community I appreciate it.
>> 
>> I have a question about the nomenclature of the annotation in the output
>> file:
>> what is the difference between genes named
>> 
>> maker-Contig-XXX
>> and those named
>> augustus-Contig-XXX-processed genes
>> ?
>> 
>> Please find attached the maker_opts file I have used for my annotation.
>> I was under the impression that the ab-initio related prefixes would be
>> present only in the genes which are not marked as "maker" in column 3 of
>> the gff file (i.e., those
>> with both ab-initio and EST evidence)
>> 
>> Is there something I am missing?
>> 
>> Thanks a lot in advance,
>> Giancarlo
>> 
>> -- 
>> Giancarlo Russo, Ph.D.
>> Functional Genomics Center Zurich
>> Y32 H66
>> Winterthurerstr. 190
>> 8057 Zurich
>> SWITZERLAND
>> Phone: +41 44 635 39 64
>> Fax: +41 44 635 39 22
>> E-Mail: giancarlo.russo at fgcz.ethz.ch
>> 
> 
> <maker_opts.ctl>