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

[Carson Holt]

All I did was supply the cDNA to est= and the scaffolds to genome=.  All the
other parameters I just used the default, then I ran MAKER.  I am using
version 2.30.

Thanks,
Carson


From:  Xin Huang <xh33 at georgetown.edu>
Date:  Wednesday, November 13, 2013 at 8:45 PM
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,

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.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 



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