[maker-devel] missing est2genome annotation

[Carson Holt]

Sorry for the slow reply.  I'm just getting back after traveling.

That's a percent coverage flag.  You can set a percent coverage threshold
in the maker_bopts.ctl file.  Partial high scoring alignments can be
common.  If you only filter by expect score, you would be surprised to see
how many ugly and confusing all the alignments become.

Thanks,
Carson

On 12-05-23 1:14 PM, "Thomas Hackl" <thomas.hackl at uni-wuerzburg.de> wrote:

>Hi again,
>
>I did some source code digging and caught the following line burying my
>exonerate alignments. I suspect it does so for a very good reason,
>therefore it would help me a lot if someone could explain to me, what is
>going on there.
>
>
>/lib/GI.pm  l.1473
>next if $e->pAh<  $pcov;
>
>
>Regards
>Thomas
>
>
>Am 23.05.2012 14:01, schrieb Thomas Hackl:
>> Hi,
>>
>> I used maker to annotate genomic contigs and among other stuff
>> provided transcripts from the transcriptome as est evidence. Blast and
>> exonerate work fine and produce valid alignments, the alignment files
>> exist in theVoid and look very good. Unfortunatly neither the
>> evidence_0.gff nor the final .gff carry the corresponding feature
>> annotations.
>>
>> Any ideas why?
>>
>> Regards
>> Thomas
>>
>
>
>-- 
>Thomas Hackl
>Julius-Maximilians-Universität
>Department of Bioinformatics
>97074 Würzburg, Germany
>Fon:  +49 931 - 31 86883
>Mail: thomas.hackl at uni-wuerzburg.de
>
>
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