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

[Xin Huang]

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
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