minas

Also if i use famdb.py to extract vertebrate specific repeats. .. they will include repeats from both Dfam and Repbase libraries, as i configured repeatmasker with both of them? Thanks

Thanks, I followed your suggestion for repeat masking in two rounds ... I did round 1 with the species option, and used the masked genome as input for another round...

Also, I have compared the two masked files, I see some sequences that were masked in the first round(with specie) were unmasked in the second round (with the custom library)....

Also is the masked genome from the second round can be used for genome annotation? or it will be missing the masking from the first round and I will have...

Just to be more clear: Results from round 1: (species specific[in this specific case its teleost]) _file name: v2.fa sequences: 26 total length: 606289673 bp (606099673 bp excl N/X-runs) GC...

the problem still persists I downloaded it again today. should i get it form github instead of https://www.repeatmasker.org/RepeatMasker/ ?