[maker-devel] basic question on maker

[Michael Campbell]

Hi Karen,

Just a quick clarification, MAKER doesn’t predict the rRNAs. If you give MAKER the rRNA sequence with the O-methylation sites it will run snoscan to predict snoRNAs. 

Take care,
Mike
> On Jan 15, 2016, at 2:39 PM, hcma <hcma at uci.edu> wrote:
> 
> 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
> 
> 
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