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/ _______________________________________________ Artemis-users mailing list Artemisfirstname.lastname@example.org http://lists.sanger.ac.uk/mailman/listinfo/artemis-users