Repeats detection in a genome

Question

[Ric]

Hi, I would like to detect repeats in my genome and I did the following steps:

> conda activate repeats
> BuildDatabase -name Repeats ragoo.fasta
> RepeatModeler -database Repeats -pa 3

Unfortunately, I do not know whether the above steps are correct and how is it possible to include Dfam ( https://www.dfam.org/releases/Dfam_3.1/families/Dfam.hmm.gz )? Additionally, how to include RepeatMasker after RepeatModeller?

Thank you in advance,

[lieven.sterck]

softmasking (or hard masking) has nothing to do with the way you detect repeats, it's just ho you mask the genome afterwards.

what you mention here is mainly to detect (de-novo) repeats in your genome. Afterwards you will need to get the resulting repeats and use them to mask the genome

[GenoMax]

Aren't those hidden markov models you are linking to?

[Ric]

Yes, I would like to detect (de-novo) repeats in your genome. Therefore, I changed my question above.

Answer 1

[Juke34]

You are mixing two different steps.

1 - Creating a repeat library (what you perform using RepeatModeler (in some steps RepeatMasker can be used to e.g classify the repeat in your library))

2 - Using repeat library/libraries to mask a genome (What you perform using RepeatMasker) You can use a de-novo repeat library made with RepeatModeler and/or You can use Repbase and/or Dfam

How to include Dfam? From here

Download the Dfam.hmm.gz library from http://www.dfam.org and save it to the RepeatMasker/Libraries directory. Uncompress the file before using RepeatMasker. The RepeatMasker distribution contains the Dfam 2.0 library.

So if yo have installed it using conda it should be save here ${CONDA_PREFIX}/share/RepeatMasker/Libraries

Answer 2

[colindaven]

This tutorial on biostars looks appropriate ! Create de novo repeat library