[maker-devel] SNAP scores and AED scores

[Barry Moore]

Hi Masa,

Also, if you want additional SNAP output that hasn't been passed forward in MAKER you can alway access the original SNAP output files in the MAKER datastore.  This is a directory structure created by MAKER to store contig specific data.  There is a datastore directory (and a corresponding index file) in the make output directory.  The index file will provide the path to individual contigs and in that contig specific directory there is a directory call theVoid.  This contains all of the output of each program that MAKER runs.

B

On Feb 13, 2014, at 1:11 PM, Carson Holt wrote:

> No.  Snap genes do not disappear. All SNAP ab initio calls will always be
> kept as reference fetters marked snap_masked (for repeat masked genome)
> and snap (for unmasked genome).  MAKER then runs SNAP another time where
> it feeds hints to SNAP based on EST and protein alignment evidence.  These
> hint based models can then compete against the ab initio SNAP models to be
> promoted to genes if their AED scores are better.  Fianl models can also
> get UTR added based on EST evidence.  That is why you can get models from
> MAKER that do not match the original SNAP ab initio calls.
> 
> So in summary, all SNAP ab initio models will be in snap_masked.  The
> MAKER models will consist of hint based SNAP rerun plus SNAP ab intio
> models processed to add UTR.
> 
> Thanks,
> Carson
> 
> 
> 
> On 2/13/14, 3:17 AM, "Masa Roller" <masa at bioinfo.hr> wrote:
> 
>> Dear all,
>> 
>> I ran snap2 based gene prediction through maker.
>> 
>> In the resulting gff file, in the source "snap_masked" I can find the
>> score in the score column of every snap prediction that did not get
>> promoted to a maker gene. This would be the score of how well the
>> prediction matches the HMM?
>> 
>> It seems to me that those snap models that are given gene status no
>> longer appear as snap_masked source but only as source "maker". Maker
>> then removes the score column, instead giving AED and eAED scores (which
>> are more about how the model corresponds to the evidence). When viewing
>> the maker transcripts and SNAP predictions in a browser, they do not
>> match (mostly, maker predictions are longer).
>> 
>> I am interested in the score of individual gene predictions that
>> underlined maker gene models. Where could I find that information?
>> 
>> Many thanks!
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140213/4966ce40/attachment-0003.html>