Running without species but including dfam+repbase

[ucabuk]

Hi,

I was wondering If it is possible to run RepeatMasker without species ? Actually, I am a bit confused because I am currently using dfam+repbase and wanted to include all families in these databases. However, when I run RepeatMasker, homo sapiens is chosen as a default species though I do not use or specify species.. How could I handle it ? If it is not possible, Can I choose more than one taxa, like Viridiplantae kingdom or combination of Oryza, Arabidopsis, and other plant taxa. Thanks.

[jebrosen]

Hello,

The default species is indeed homo sapiens. You can change this with the -species option, which accepts either a leaf species or a single clade such as Viridiplantae or Arabidopsis, or even Eukaryota.