AnnotationFinalizer for renaming genes and transcripts about jstacs HOT 2 CLOSED

Hi Steve,

Thanks for using GeMoMa.

If you like to rename genes and transcripts you have to use the parameters from the module AnnotationFinalizer:
http://www.jstacs.de/index.php/GeMoMa-Docs#AnnotationFinalizer
You can either run AnnotationFinalizer on your own or as part of teh GeMoMaPipeline. By default renaming is inactivated. To activate the renaming, you have to set AnnotationFinalizer.r. There are three different options:

• NO: which leads to no renaming
• COMPOSED: which leads to a renaming using some chromosome/contig/... infix
• SIMPLE: which leads to a renaming without using a chromsome/contig/... infix

If you chose any of the options COMPOSED or SIMPLE you have to set further parameters for the renaming, e.g., a prefix. Currently the prefix is limited to \w+ which is [a-zA-Z_0-9]+. Hence, your current prefix is not allowed due to the dot.

Some more information is given in the manual:
http://www.jstacs.de/images/c/c6/GeMoMa-manual.pdf
However, I saw that there are some formating mistakes. I'll change this for the next release.

I hope that helps. Please let me know whether you were successfully or not. If you were not sucessfully, please add the error message for better support.

best regards, Jens

from jstacs.

Jens,
thank you for your quick response. I used a value for AnnotationFinalizer.p without illegal characters and it worked fine.
-Steve

from jstacs.