[maker-devel] A suspected strange behavior of Maker...

[Xin Huang]

Hi Carson,

Thanks a lot for doing the test for me! I didn't get any annotation in the
GFF file generated by Maker even if I only used scaffold5347 as the genome
and the face EST sequence as the est evidence. Is there something that I
can modify to put the alignment into the GFF file? I used est2genome=1
option to get prediction from exonerate, but still couldn't get any
prediction.

Thanks!

Xin


On Wed, Nov 13, 2013 at 9:59 PM, Carson Holt <carsonhh at gmail.com> wrote:

> For scaffold5347 I get results from exonerate and blastn without any
> modification to default parameters.  For scaffold3928 the alignment is very
> poor, and gets filtered out.  I can force it to keep it but I have to allow
> for abnormally long introns of 65kb (introns that large are extremely rare
> in biology – as in if you took every gene from 100 organisms you might find
> a single gene among all of them with that long of an intron), and I have to
> allow for low end to end matching (less 30%).  This alignment definitely
> should have been rejected.
>
> Thanks,
> Carson
>
>
> From: Xin Huang <xh33 at georgetown.edu>
> Date: Monday, November 11, 2013 at 8:52 AM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] A suspected strange behavior of Maker...
>
> Hi Carson,
>
> Thank you very much for getting back to me on this. Sorry I was too quick
> to jump to a suspicion! Thanks for pointing it out and please see attached
> the EST (face_cDNA.fa) and genome scaffold sequences
> (albo_scaf3928+5347_for_face_cDNA.fa) I used for Maker. We used blastn to
> identify these two scaffolds for this cDNA sequence, and exonerate result
> also showed that this cDNA can be aligned to the scaffolds.
>
> Thanks!
>
> Xin
>
>
> On Mon, Nov 11, 2013 at 12:10 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Sorry for the slow reply, I was moving from Canada to the US, got sick,
>> and my moving truck got delayed one week. So I fell behind on the maker
>> list.
>>
>> What you observe is correct behavior.  The config is blasted against the
>> database of ESTs/proteins.  It really doesn't matter which way you blast,
>> you pick the direction that is most efficient for the question you are
>> asking, and you only have to adjust the Z value for database size if you
>> want alignment scores to be reproducible both ways.
>>
>> Not getting results means they were filtered out for some reason (you
>> don't even have blastn results in your output).  If you can send a test
>> dataset I can take a look and tell you which filter.
>>
>> Thanks,
>> Carson
>>
>>
>> From: Xin Huang <xh33 at georgetown.edu>
>> Date: Tuesday, November 5, 2013 2:40 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] A suspected strange behavior of Maker...
>>
>> Hi,
>>
>> I found a very bizarre thing when I ran Maker several times. The blastn
>> research seems to reverse query and subject the way it's specified in the
>> maker_opts.ctl file. When I put the scaffold sequence after genome= and the
>> cDNA sequence after est=, the blastn result actually used the scaffold as
>> query and the cDNA as subject. I realized that this sounds unreal, so I
>> reversed the places for the two and the blastn result is normal with the
>> cDNA as query and the scaffold as subject, but at the same time, the GFF
>> file is of the cDNA sequence. I tried a few times, and got the same result.
>> I deleted Maker (2.28) and reinstalled the beta version (2.30), still
>> getting the same result.
>>
>> My wild guess was that this might be the reason why the est2genome
>> prediction using the EST sequence didn't go into the GFF3 file, as stated
>> in a previous email to the Maker-devel. I couldn't figure out how to test
>> this, though. I wonder if there's anything dramatically wrong that I've
>> been doing to get such odd results... If you'd like me to send you any
>> output files or control files, please let me know and I'll promptly pass
>> those along.
>>
>> Thank you very much for considering my email.
>>
>> Sincerely,
>>
>> Xin Huang
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
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