[maker-devel] MAKER and RepeatModeler

[Shaun Jackman]

Hi, Carson.

I set model_org=picea. I see that it created a new data base in the RepeatModeler folder Libraries/20140131/picea/specieslib. What is the effect of the model_org option? Does it extract sequences from RepBase that match the string picea?

Cheers,
Shaun



-- 
http://sjackman.ca/

On 2015-July-17 at 9:40:58 , Carson Holt (carsonhh at gmail.com) wrote:

That is weird.

One thought though.  When you run MAKER do you supply both rmlib and model_org or just rmlib? If you are only supplying rmlib, you could try supplying both together (RepeatMasker will then run twice).  That way some of the edge cases might better be identified.

—Carson



On Jul 16, 2015, at 5:25 PM, Shaun Jackman <sjackman at gmail.com> wrote:

Hi, Carson.

I removed two small contaminant contigs (~7 kbp) from the assembly (~6 Mbp), and MAKER found four fewer genes, four copies of the same atp8 gene, but these genes were not in the contaminant contigs.

I figured out that it’s because I’m running RepeatModeler to create the rmlib for MAKER. When I remove the contaminant contigs, RepeatModeler now identifies this gene atp8 as being a LTR/Gypsy repeat.

Any thoughts on why removing two contigs would cause RepeatModeler to identify new repeats?

Cheers,
Shaun




-- 
http://sjackman.ca/

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