Question: repeatmasker species setting
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3 months ago
frida • 10
rome

hello! I'm working with a genome of cephalopoda. Firstly, I ran Repeatmasker with this input

 /home/RM/RepeatMasker -s -gff OB150DEC_2.fa

to analyze the genome assuming that the specie is homo sapiens. I'm not sure that it is correct, because I suppose that transposable elements could be different in invertebrates (it doesn't find Mites, for example). So I think that I have to change -species in RepeatMasker species. My doubt is about the specie that I have to set. I read in the manual:

 -species <query species>
        Specify the species or clade of the input sequence. The species name
        must be a valid NCBI Taxonomy Database species name and be contained
        in the RepeatMasker repeat database. Some examples are:

          -species human
          -species mouse
          -species rattus
          -species "ciona savignyi"
          -species arabidopsis

I don't think these are the only species to use. Where can I find the entire list of them? Thank you anyway. Bests

ADD COMMENTlink 3 months ago frida • 10 • updated 3 months ago Juke-34 ♦ 2.2k
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You can also create a custom library with RepeatModeler (there are biostars posts that you can search for to get instructions) and run that model on your cephalpod genome with RepeatMasker.

ADD REPLYlink 3 months ago
jean.elbers
♦ 1.1k
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okay, but repeatmasker will be able to recognize the library created by myself finding transposable elements? I've tried using Repeatscout, but the results didn't are the expected. Repeatmodeler is different?

ADD REPLYlink 3 months ago
frida
• 10
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I don't have experience with RepeatScout, but RepeatModeler combines the output of RepeatScout and RECON (http://www.repeatmasker.org/RepeatModeler/). I personally haven't fed a custom library from RepeatModeler to RepeatMasker, but others on biostars can probably chime in

ADD REPLYlink 3 months ago
jean.elbers
♦ 1.1k
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okay, thank you for your help!

ADD REPLYlink 3 months ago
frida
• 10
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I think there are also:

Other commonly used species:

mammal, carnivore, rodentia, rat, cow, pig, cat, dog, chicken, fugu,
danio, "ciona intestinalis" drosophila, anopheles, elegans,
diatoaea, artiodactyl, arabidopsis, rice, wheat, and maize

To use the library identified from your own genome, you might have a look at this document (RepeatModeler+RepeatMasker): https://blaxter-lab-documentation.readthedocs.io/en/latest/repeat-masking.html

ADD REPLYlink 3 months ago
SMK
♦ 1.3k
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3 months ago
Juke-34 ♦ 2.2k
Sweden

Using queryTaxonomyDatabase.pl -h and queryRepeatDatabase.pl -h scripts you should find what you want. They are in the util folder coming with repeatmasker.

ADD COMMENTlink 3 months ago Juke-34 ♦ 2.2k
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If I put

 `~/RM/RepeatMasker/util$ queryRepeatDatabase.pl -h` ,

it says to me

queryRepeatDatabase.pl: command not found
ADD REPLYlink 3 months ago
frida
• 10
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do ls -l in the util folder to see what script is there (copy the result here). What version of repeatmasker do you have?

ADD REPLYlink 3 months ago
Juke-34
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~/RM/RepeatMasker/util$ ls -l
totale 204
-rwxr-xr-x 1 fragua fragua  4622 nov 21  2018 buildRMLibFromEMBL.pl
-rwxr-xr-x 1 fragua fragua 22868 nov 21  2018 buildSummary.pl
-rwxr-xr-x 1 fragua fragua 10430 nov 21  2018 calcDivergenceFromAlign.pl
-rwxr-xr-x 1 fragua fragua 20607 nov 21  2018 createRepeatLandscape.pl
-rwxr-xr-x 1 fragua fragua 38299 nov 21  2018 dupliconToSVG.pl
-rwxr-xr-x 1 fragua fragua  8659 nov 21  2018 getRepeatMaskerBatch.pl
-rwxr-xr-x 1 fragua fragua 16586 apr 29 22:43 queryRepeatDatabase.pl
-rwxr-xr-x 1 fragua fragua  4362 apr 29 22:43 queryTaxonomyDatabase.pl
-rwxr-xr-x 1 fragua fragua  4242 nov 21  2018 rmOut2Fasta.pl
-rwxr-xr-x 1 fragua fragua  3693 apr 29 22:43 rmOutToGFF3.pl
-rwxr-xr-x 1 fragua fragua 19180 apr 29 22:43 rmToUCSCTables.pl
-rwxr-xr-x 1 fragua fragua 12725 nov 21  2018 trfMask
-rwxr-xr-x 1 fragua fragua  7735 nov 21  2018 wublastToCrossmatch.pl

The version of RM is RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley

ADD REPLYlink 3 months ago
frida
• 10
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1

You can try (when you're in ~/RM/RepeatMasker/util):

./queryRepeatDatabase.pl -h
ADD REPLYlink 3 months ago
SMK
♦ 1.3k
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yes as say SMK then adding ./ in front should be enough. It will execute it. Or you could as well do perl queryRepeatDatabase.pl -h

ADD REPLYlink 3 months ago
Juke-34
♦ 2.2k

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