Detecting and masking repeats with EDTA: Low threshold vs complete masking

Question

[zhtsandres]

So I ran EDTA on my genome and got 39% of repeats, then this program also generated a masked copy ready to use in Maker, but only masking repeats > 1kb, resulting in only 20% of the total genome masked. Why would the EDTA perform a low threshold masking? Does it have any advantage over a complete masking?

Answer 1

[jaredbernard]

In the new tutorial for EDTA (DOI: 10.1007/978-1-0716-1134-0_4), Su et al. say the Maker version is masked at a lower threshold to facilitate gene predictions. But Maker already has a "soft masking" feature, so I'm not sure if this is necessary. Maybe you should ask Ou Shujun by starting an issue on his GitHub site. Honestly, I wonder if the EDTA output fasta file is sufficient for Maker.