[maker-devel] Questions about re-annotating

[Cook, Malcolm]

Hi,

I am re-running an analysis after having adding `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of work is re-done.

When I re-run maker, should I provide any additional options.  In particular, either "--again" ?

On this subject, I read in http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data

"if you are using est_gff= you don't even have to repeat mask."  - does this mean I should always run maker with option -RM_off when updating annotation?

On a related note, if I have est2genome turned on, what changes to configuration should cause exonerate to run?  I'm guessing:
  adding new est= files
  turning on alt_splice=1

Thanks!

~ malcolm_cook at stowers.org