Repetitive regions annotation

Question

[frarodmar17]

I am trying to annotate repetitive regions using a pipeline based on RepeatModeler and RepeatMasker. However, I am not sure if I should perform an intermediate step between RepeatModeler and RepeatMasker functions.

Answer 1

[samuel.a.odonnell]

I think in most cases the repeatmodeler library will be used directly to mask a genome with repeatmasker.

However if it is early days you might want to look at using a tool like EarlGrey which tries to improve the repeatmodeler output before masking (alongside having automating all these steps, adding analyses, making life easier etc).