about RepeatMasker command line

Question

[wayma]

Hello everybody!

Please I'd like to use repeatMasker to look for one special family of transposable elements that's why I want to use my sequences (fasta file) as query to look for in the genome of a known insect

who can tell me what's the command line to put to mask elements using my own sequences please?

I can't put -species (genome) and -lib options at the same time! so what should I do?

Thank you very much

[bostanict.net]

following this topic, I have a question. What if I want to only mask my sequences and not the sequences in the master db of RepeatMasker.

when I use -lib, it will mask my sequences + the RepeatMasker db right? What id I do not want the second one. Can anyone tell me how to run the command to use only my own db?

thanks

[lieven.sterck]

not a 100% sure but i think that when you use the -lib option it will not use the build-in DBs

[201314918]

Hi guys. I am struggling with RepeatMasker. I have installed it successfully but now I want to Run it, but I don't have a clue of what command should I use. I tried to follow the above commands "-lib" and -species" and it says " command not found".

How I do it? I open the repeatmasker directory and type the above commands.

Please help me guys I am new in this computer language.

[susan.klein]

Sorry this is not helpful, just an observation.. the RepeatMasker website is horrible - I could not find any information about running command line there and there is no documentation on their git. The link on their page to running locally does not work - just sends to bottom of page. https://www.repeatmasker.org/webrepeatmaskerhelp.html#contacts

Answer 1

[SES]

Just use -lib for a custom library. If you specify -species then RepeatMasker will mask with just the library of repeats for the species you specify. The latter option speeds up the masking if you have a model system (or a closely-related species). Using -lib tells RepeatMasker to use the full RepeatMasker library plus the library you specify, but the masking behavior can be changed at the command-line (e.g., to only mask interspersed repeats, or not mask interspersed repeats, etc.).

[wayma]

thank you very much SES. It's clearer now! but which option should I put in order to specify the genome in which I'll mask interspersed repeats?

[SES]

Typically you would mask all types and check the results, but if you are only interested in interspersed repeats then you can use the "-int" option.

[wayma]

ok so let's summarize : I'm looking for transposable elements belonging to a special subfamily in the genome of an insect so I've to do like this:

RepeatMasker -lib (file containing the transposable elements that I'd like to use as query to mask elements in the genome) -int (to focus on interspersed repeats) isn't?

The problem is what am I going to mask? in which genome sequences? I have to indicate the file of the genome that I'll mask with my own library of tranposable elements, isn't it?

thank you again

Answer 2

[lieven.sterck]

you should be able to run something like this :

RepeatMasker -lib <fasta file of repeats to mask>  <seqfiles(s) in fasta format>

you only need to add the -species if you specifically want to use a lib constructed for any of the species offered by repeatmasker