augustus exon calling ~

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

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)


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

This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.
maker-devel mailing list
[hidden email]

artemis01.png (222K) Download Attachment
artemis02.png (129K) Download Attachment