Tim et al,

I've just run some MAKER2 annotations on a small parasite genome
(eukaryotic)., producing a GFF3 file. About 70% of the genes have
phase=0 (GFF column 8), while 15% have phase=1 and 15% have phase=2.
Artemis seems to load it (mostly) fine, and puts
/codon_start=(phase+1) tags.

However, when viewing, all the genes look fine on the +strand no
matter the phase, but the (some of the?) non-zero phase ones
(/codon_start 2 or 3) on the -strand seem to render incorrectly, with
the exons being out of frame.

I've looked through the mailing list archives, and found one reference
to a similar problem, but it appeared to be resolved, but I've
reproduced it somehow. I'm using Artemis 14.0.11. I'm also getting
possibly related warnings - about 100 x "RANGE NOT FOUND xxxx..yyyyy".

Any help appreciated!

-- 
--Dr Torsten Seemann
--Scientific Director : Victorian Bioinformatics Consortium, Monash
University, AUSTRALIA
--Senior Researcher : VLSCI Life Sciences Computation Centre,
Parkville, AUSTRALIA
--http://www.bioinformatics.net.au/

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