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
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written
by
wayma •
2 answers
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.).
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
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
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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
not a 100% sure but i think that when you use the -lib option it will not use the build-in DBs
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.
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