Hi, I would like to remove and add a sequence to the repeatmasker library.

I tried extracting the fasta sequence to remove and add the sequence that I wanted by converting the embl to a fasta:

perl util/buildRMLibFromEMBL.pl Libraries/RMRB.embl > embl_converted_fasta/RMRB.fasta

then running the lib parameter:

RepeatMasker -pa 24 -gff -lib "$lib" -dir "$out" "$file" -e ncbi

However, I am doubtful with my result as some repeats are not specific to my species. This is also because my lib contains all the repeat consensus from the repeatmasker library. For example, I have two repeats in tandem, one from my target species, one from a related species, however, upon running blastn to the two repeats, they are basically the same repeats.

Can you help me how I can run repeatmasker with the -species option and with modified library?

Thank you!