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

[Carson Holt]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20131110/153ea1e5/attachment-0003.html>