[maker-devel] basic question on maker

[hcma]

Hi Carlson,

Regarding non-coding RNA predictions, MAKER only predicts tRNAs and 
rRNAs, but not other RNAs, for example, lncRNAs?

Thanks again.

Best Regards
Karen




On 2016-01-15 09:16, Carson Holt wrote:
>> Can maker2 be run without inputting any protein sequences?
> 
> Yes. But it will not perform as well.
> 
>> How to turn this off in the control files?
> 
> Any option left blank is off.
> 
> 
>> Also, can i run maker using Augustus and not SNAP? Again, how do i 
>> turn SNAP off?
> 
> Yes. Leave it blank.
> 
> 
>> Does maker also predict non-coding genes?
> 
> You can run it with tRNAscan or snoscan. Snoscan requires you to have
> rRNAs from your organism to train with though.
> 
> —Carson