[maker-devel] repeats masking

[Carson Holt]

You don’t need to worry about redundancy.

—Carson

> On Aug 30, 2017, at 8:01 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Dear Carson:
> 
> Thank you again for all you valuable suggestions. Now I am generating the species specific repeat library. I wonder whether I need to remove the masked the regions by existing repeatMasker library, before I run repeatModeler? I think there may be some redundancy if I run  repeatModeler directly on the genome and then use both existing repeatMasker library and the repeatModeler library to mask the genome. Does it matter, if there is such redundancy?
> 
> Thanks
> 
> Best
> Quanwei
> 
> 2017-08-23 14:10 GMT-04:00 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>:
> 
>> (1) For the predicted unknown (unclassified) repeat sequences (those in Modelerunknown.lib), it mentioned "Sequences in Modelerunknown.lib were searched against a transposase database (derived from RepeatMaske <http://www.repeatmasker.org/>r) and sequences matching transposase were considered as transposons belonging to the relevant superfamily".  
>> I wonder how to do this search. Annotate the "unknown" repeat sequences using the Repeatmaker? Then what to do, if for an "unknown" repeat sequence, only part of the sequence match the known repeat elements.
> 
> You can use RepBase match I guess, but I would not be overly worried about classification. MAKER won’t use any classification info you give it.
> 
> 
>> (2) To exclude gene fragments, I need map the predicted repeat sequences against a protein database, and then run the package "ProExcluder". Right?  I wonder how to get such protein database. Since I am working on a new rodent species, can I use all the rodent proteins from Uniprot (both Swiss-Prot and TrEMBL)?
> 
> Try Swiss-Prot. That is a well curated cross species set.
> 
> 
>> (3) After I generate the species specific repeat library, do I still need to select a model organism for RepBase masking (as shown below). 
>> 
>> In the file "maker_opts.ctl"
>> #-----Repeat Masking (leave values blank to skip repeat masking)
>> model_org=Mammalia #select a model organism for RepBase masking in RepeatMasker
>> rmlib=myRepeat.fa #provide an organism specific repeat library in fasta format for RepeatMasker
> 
> Yes. Supply both.
> 
> 
> —Carson
> 

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