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

Question

[mt1022]

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

Answer 1

[GenoMax]

Here.

[mt1022]

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.

[GenoMax]

You can email UCSC browser tech support and ask ([e-mail]).

[mt1022]

hi, following the archives by [e-mail], 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!