How To Build Combined Library For Repeatmasker?

Question

[SK]

Thanks for your attention. I want to to perform repeatmasking on ant genome. Ant is also included in the repeat library obtained from Repbase. The library RepeatMaskerLib.embl also contains my species. However, I also generated de novo repeat library by repeatmodeler (consensi.fa). How can I use both library for masking ant genome ? Should I concatenate RepeatMaskerLib.embl and consensi.fa or can I use both library with single command?

Answer 1

[SES]

I would start by checking how your library and the RepeatMasker library differ. In the util directory of RepeatMasker there is a script called queryRepeatDatabase.pl and this will tell you all the repeats in the database for a given species. You can obviously skip that step if you know your library is different. When you run RepeatMasker, just use the -lib option to specify your own file. I would not try to concatenate the files because they are different formats. If you want to use the full RepeatMasker library with your repeats, you could convert the RepeatMasker library to fasta, then concatenate the files and run the program with the -lib option. There is a script called buildRMLibFromEMBL.pl in the util directory of RepeatMasker for converting their version of the EMBL format to fasta.