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

[Xin Huang]

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
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>
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