I'm working with a genome of cephalopoda. Firstly, I ran Repeatmasker with this input
/home/RM/RepeatMasker -s -gff OB150DEC_2.fa
to analyze the genome assuming that the specie is homo sapiens.
I'm not sure that it is correct, because I suppose that transposable elements could be different in invertebrates (it doesn't find Mites, for example).
So I think that I have to change
-species in RepeatMasker species. My doubt is about the specie that I have to set. I read in the manual:
-species <query species>
Specify the species or clade of the input sequence. The species name
must be a valid NCBI Taxonomy Database species name and be contained
in the RepeatMasker repeat database. Some examples are:
-species "ciona savignyi"
I don't think these are the only species to use. Where can I find the entire list of them?
Thank you anyway.