[maker-devel] For help about masking repeats before annotation

[Michael Campbell]

Hi Chao Chao,

I’m not sure how to trouble shoot this if there were no error messages. I’ve ccd a couple of people that have worked with this protocol much more than I have.

Ning and Kevin,
Do you have any tips for running these tools that may help Chao Chao?

Thanks,
Mike
> On Mar 15, 2017, at 8:48 AM, dcg at cau.edu.cn wrote:
> 
> Thank for your reply!
> I just followed the guide iat http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced> 
> 
> To use LTRHarvest, my command is as below(the filename was set for my favor)
> DIR1/gt suffixerator -db seqfile -indexname seqfileindex -tis -suf -lcp -des -ssp –dna
> DIR1/gt ltrharvest -index seqfileindex -out seqfile.out99 -outinner seqfile.outinner99 -gff3 seqfile.gff99 -minlenltr 100 \
> -maxlenltr 6000 -mindistltr 1500 -maxdistltr 25000 -mintsd 5 -maxtsd 5 -motif tgca -similar 99 -vic 10  > seqfile.result99
> No error, but no results as well
> 
> Chao Chao
> 2017.03.15
>  
> From: Michael Campbell <mailto:michael.s.campbell1 at gmail.com>
> Date: 2017-03-15 10:27
> To: dcg <mailto:dcg at cau.edu.cn>
> CC: maker-devel <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] For help about masking repeats before annotation
> Hi Chao Chao,
> 
> I’ve not run into this before. Could you post the RepeatModeler command you used?
> 
> Thanks,
> Mike
>> On Mar 5, 2017, at 6:26 AM, dcg at cau.edu.cn <mailto:dcg at cau.edu.cn> wrote:
>> 
>> Dear sir:
>>        Before the maker opeations, I do repeat masking first on my contigs. 
>>        However , when I followed " Repeat Library Construction-Advanced ",  no results generated after I running LTRharvest. So I couldn't do any further.
>>        
>>        When I attempted to follow" Repeat Library Construction-Basic " to run RepeatModeler, a note caused my attention even though RECON can return some results :
>>        NOTE: RepeatScout did not return any models.
>> 
>>        Is the situation above normal in masking progress? How can I deal with the problems to make a high-quality repeat library for my assemblied contigs?
>> 
>>        Hope to hear from you.
>>        Best wishes!
>> 
>> Chao Chao
>> 2017.03.05
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