This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Repeats detection in a genome

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,

assembly genome annotation
• 2,563 views • link
updated by Juke34 Juke34 • written by Ric Ric

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by Ric Ric

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

• 0 views • link
written by lieven.sterck lieven.sterck

2 answers

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

• 0 views • link
written by Juke34 Juke34

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

• 0 views • link
written by colindaven colindaven

Log in to answer this question.

More posts like this