repeatmasker species setting

Question

[Chironex]

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

[jean.elbers]

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.

[Chironex]

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?

[jean.elbers]

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

[Chironex]

okay, thank you for your help!

[AK]

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

Answer 1

[Juke34]

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

[Chironex]

If I put

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

it says to me

queryRepeatDatabase.pl: command not found

[Juke34]

do ls -l in the util folder to see what script is there (copy the result here). What version of repeatmasker do you have?

[Chironex]

~/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

[AK]

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

./queryRepeatDatabase.pl -h

[Juke34]

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

[Picasa]

I would like to know all the insects present, is there a way to have the list ?

I used

queryTaxonomyDatabase.pl -species "Insecta"

but it just display:

RepeatMasker Taxonomy Database Utility
======================================
Species = Insecta
Lineage = Insecta
          Hexapoda
          Pancrustacea
          Mandibulata
          Arthropoda
          Panarthropoda
          Ecdysozoa
          Protostomia
          Bilateria
          Eumetazoa
          Metazoa
          Opisthokonta
          Eukaryota
          cellular organisms
          root