I am doing repeat elements annotation for a new genome. From what I read online and in papers, the work flow is 1) Dustmasker, 2) Trf, 3) RepeatModeler and 4) RepeatMasker.
I just finished masking the low complexity regions using Dustmasker. Should I use the hard masked file as input for Trf, or use the original genome sequence file as input? Is it ever a good idea to use a masked sequence as input for another repeat masking program?
Thank you very much!