[maker-devel] Maker predicting fusion genes?

[Mikael Brandström Durling]

Ok, do you by that imply that the predictions that end up in the gff3 output from the ab initio predictors (snap_masked, augustus_masked, and genemark), are not the final hinted predictions? Otherwise, I’m sorry that I can’t follow your reasoning. I checked my gff file, and there is no evidence there to support the bridge, as far as I can tell (See attached gff of the region or http://figshare.com/articles/Maker_prediction/942301 where all evidence is plotted).

Mikael



23 feb 2014 kl. 21:00 skrev Carson Holt <carsonhh at gmail.com>:

> The image doesn’t show all evidence sources, but the short answer is that
> one of you evidence sources (est2genome, protein2genome, or blastx)
> bridges the two regions, and when provided the bridged hint one of the
> gene predictors thinks it makes sense to create a single model instead.
> my guess is that it’s blastx evidence.
>
> —Carson
>
>
> On 2/23/14, 9:57 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
> wrote:
>
>> Dear list and maker developers,
>>
>> I was browsing the results of a recent maker run, focusing on differences
>> between this run with the a recent maker (svn r1067) and a previous run
>> with svn revision 1022 (I recall). One of the differences I found was a
>> gene lost in the new prediction set, but replaced by an extended version
>> of a previous neighbor (see
>> http://figshare.com/articles/Maker_prediction_comparison/942300).  As you
>> can see, there is no support for the join in the evidence. Do you have
>> any clue to what might cause this?
>>
>> Best regards,
>> Mikael Durling
>>
>>
>>
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>
>

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