[maker-devel] MAKER and RepeatModeler

[Carson Holt]

The subset is actually built of a built of a taxonomy. So you can extract all repeats for a species or genus for example. If a term doesn’t match the internal taxonomy, it throughs an error.

—Carson

> On Jul 17, 2015, at 11:24 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 
> Yes. It takes a the subset of RepBase. If runtime isn’t an issue and you really want to mask as much as possible, you can also set model_org=all.  Most of whatever else is in RepBase probably won’t align anywhere, but it may give you marginally better sensitivity.
> 
> —Carson
> 
> 
> 
>> On Jul 17, 2015, at 11:20 AM, Shaun Jackman <sjackman at gmail.com <mailto:sjackman at gmail.com>> wrote:
>> 
>> 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/ <http://sjackman.ca/>
>> On 2015-July-17 at 9:40:58 , Carson Holt (carsonhh at gmail.com <mailto: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 <mailto: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/ <http://sjackman.ca/>
>>> 
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>>> 
>> 
>> 
> 

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