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where can I get the parameters used by UCSC genomes to run RepeatMasker for dm6?

where can I get the parameters used by UCSC genomes to run RepeatMasker for dm6? I searched FAQ but didn't find the answer.

ucsc repeatmasker
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updated by GenoMax GenoMax • written by mt1022 mt1022

1 answer

Here.

• 1 views • link
written by GenoMax GenoMax

Thanks. I am interested in whether UCSC genome browser will additionly use the '-species' parameter to specify the species/clade or only use '-s' for all species as it is not mentioned in the FAQ. I am not sure whether '-species' parameter will improve the results.

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written by mt1022 mt1022

You can email UCSC browser tech support and ask (genome@soe.ucsc.edu).

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written by GenoMax GenoMax

hi, following the archives by genome@soe.ucsc.edu, I find the answer after looking up similar posts.

how ucsc do RepeatMasker

my $defaultSpecies = 'scientificName from dbDb';
my $species = $opt_species ? $opt_species : &HgAutomate::getSpecies($dbHost, $db);

Thanks for your help!

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written by mt1022 mt1022

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