augustus exon calling ~

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augustus exon calling ~

Salim Bougouffa-2
Hi Maker folks,

I have several issues with a plant genome annotation that I am currently doing but perhaps the most recurrent issues are:

1/ CDSs that are missed where significant rna-seq evidence is there (figure artemis01)
2/ vice versa where one or two exons are added without rna-seq evidence/intron hints (figure artemis02)

info about the runs:
1/ using augustus with a pre-existing model for a related plant that has high homology to the one I am annotating
2/ umask=1 (seems to do better than umask=0; is this a good thing to do)
3/ evm = 1 (seems to perform better than emv=0)
4/ repeatmasking (denovo + repbase)

Best,
/SB


_______________________________________________________
Salim Bougouffa(PhD), Postdoctoral Fellow
4700 KAUST, CBRC, Blg3. Office4326-WS05,
Thuwal, Jeddah, KSA, 23955-6900
(966) 012 808 2963 || [hidden email]


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