[maker-devel] MAKER start with masked genome

[Carson Hinton Holt]

There are two ways.  First rerun in the same working directory. MAKER will reuse previous repeat masking files as long as repeat masking settings did not change between runs. Second, if you have a genome wide GFF3 from the previous run, you can pass it in as maker_gff and set the appropriate pass=1 option underneath for repeats.

—Carson

Sent from my iPhone

> On Apr 11, 2018, at 6:22 AM, Mark Yandell <myandell at genetics.utah.edu> wrote:
> 
> 
> 
> On 4/11/18, 5:08 AM, "Jonas Bohn" <bohnj at uni-muenster.de> wrote:
> 
>    Dear MAKER developers,
> 
>    I`m a master student in a bioinformatics group of university of muenster and I want to use MAKER for genome Annotation of an Ant genome. I ran  RepeatMasker before and it took some days to get a masked genome. So I try to save some time for my master thesis. My question is: Is there an option to run MAKER2 without running RepeatMasker again (skip the RepeatMasker step)?
> 
>    I`m looking forward to hearing from you.
> 
>    Best regards,
> 
>    Jonas Bohn
> 
>    MSc. Student
>    Evolutionary Bioinformatics
>    University of Muenster, Germany  
>