Detecting and masking repeats with EDTA: Low threshold vs complete masking
1
0
Entering edit mode
3 months ago
zhtsandres • 0

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?

repeat masker. annotation genome EDTA • 226 views
ADD COMMENT
1
Entering edit mode
10 weeks ago
jaredbernard ▴ 20

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.

ADD COMMENT

Login before adding your answer.

Traffic: 830 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6