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Repetitive regions annotation

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.

repeatmodeler repeatmasker
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updated by samuel.a.odonnell samuel.a.odonnell • written by frarodmar17 • frarodmar17

1 answer

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).

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written by samuel.a.odonnell samuel.a.odonnell

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