[maker-devel] basic question on maker

[Daniel Ence]

Hi Karen,

I don’t of a unified tool that predicts lncRNAs from genomic sequence. I found a tool that predicts lncRNAs from RNAseq dataset, which you might be able to use for your project. I’ve never used it, but it might be a starting place. http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-311

Here’s also a review that describes several workflows for annotating lncRNAs in insect genomes: http://www.sciencedirect.com/science/article/pii/S2214574515000061

Hope that helps,
Daniel



Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

On Jan 15, 2016, at 3:39 PM, hcma <hcma at uci.edu<mailto: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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