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I'm analyzing mygenome.fa with RepeatScout and RepeatMasker to find transposable elements. I produced a library of Repetitive elements with repeatscout and the I masked TE using Repeatmasker. 

./build_lmer_table -l 14 -sequence mygenome.fa -freq mygenome.freq
./RepeatScout -sequence mygenome.fa -output mygenome_repeats.fa -freq mygenome.freq -l 14
cat mygenome_repeats.fa| ./filter-stage-1.prl >mygenome_repeats_filtered1.fasta
./RepeatMasker -s -lib mygenome_repeats_filtered1.fa mygenome.fa

Generate a masked genome using (non-low-complexity, non-tandem) repeats

cat mygenome_repeats_filtered1.fa | ./filter-stage-2.prl --cat mygenome.fa.out >mygenome_repeats_filtered2.fa

Filter out all (non-low-complexity, non-tandem) repeats that have less than 10 repeats

./RepeatMasker -pa 4 -s -lib mygenome_repeats_filtered2.fa -nolow -norna -no_is -gff mygenome.fa

After this I ran Repeatmasker: 

./RepeatMasker no_is mygenome_repeats_filtered2.fa

and I produced:

mygenome_repeats_filt2.fa.masked  mygenome_repeats_filt2.fa.tbl
mygenome_repeats_filt2.fa.cat  mygenome_repeats_filt2.fa.out

I would to know a way to find the location of transposable elements masked by RepeatMasker on my genome.

Supposing that this is a part of my Repetitive elements library produced with RepeatScout as I showed above:

less mygenome_repeats_filt2.fa

>R=3 (RR=4.  TRF=0.000 NSEG=0.000)
TAAGGCGGCGAGCTGGCAGAATCGTTAGCACGCCGGGCGAAATGCTTAGCGGTATTTCGTCTGTCTTTACGTTCTGAGTT
CAAATTCCGCCGAGGTCGACTTTGCCTTTCATCCTTTCGGGGTCGATAAAATAAGTACCAGTTGAGCACTGGGGTCGATG
TAATCGACTTACCCCCTCCCCCAAAATTTCTGGCCTTGTGCCTATATTAGAAACGATTATT
>R=4 (RR=5.  TRF=0.122 NSEG=0.226)
ACACACACACACACACACACACACACATATATATATATATACATATATACGACGGGCTTCTTTCAGTTTCCGTCTACCAA
ATCCACTCACAAGGCTTTGGTCGGCCCGAGGCTATAGTAGAAGACACTTGCCCAAGGTGCCACGCAGTGGGACTGAACCC
GGAACCATGTGGTTGGTAAGCAAGCTACTTACCACACAGCCACTCCTGCGCCTATATATAT
>R=6 (RR=7.  TRF=0.134 NSEG=0.247)
TTGTTTCAGTCATTTGACTGCGGCCATGCTGGAGCACCGCCTTTAGTCGAGCAAATCGACCCCAGGACTTATTCTTTGTA
AGCCTAGTACTTATTCTATCGGTCTCTTTTGCCGAACCGCTAAGTTACGGGGACGTAAACACACCAGCATCGGTTGTCAA
GCGATGTTGGGGGGACAAACACAGACACACAAACACACACACACACATACATATATATATATATATATATA

from the file mygenome_repeats_filt2.fa.out I can see that in R=3 there is a trasposable element:

   SW   perc perc perc  query     position in query    matching        repeat              position in repeat
score   div. del. ins.  sequence  begin end   (left)   repeat          class/family      begin  end    (left)  ID

348   20.6  0.0  0.0  R=3          78   140   (81) + AmnSINE2        SINE/tRNA-Deu         67    129  (229) 234

As you can see I have the coordinates to find this element in the library, but I would to find its exactly in the file that contain my assembled genome.

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  • 1
    $\begingroup$ Hi. In order to help you better could you explain what have you tried to do this? This way our answers can explain how to find the solution (not only the solution itself) or how to improve your skills. $\endgroup$
    – llrs
    May 9, 2019 at 13:12
  • $\begingroup$ ok, I modified the answer :) $\endgroup$
    – jonny
    May 9, 2019 at 13:30
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    $\begingroup$ Great edit!! But this code does not show what you tried to "find the location of transposable elements masked by RepeatMasker" (or at least is not clear enough for me that I am not familiar with RepeatMasker). $\endgroup$
    – llrs
    May 9, 2019 at 13:47
  • $\begingroup$ sorry,I'll modified again the answer and I'll try to specify it better $\endgroup$
    – jonny
    May 9, 2019 at 13:48
  • 1
    $\begingroup$ I modified the file with some other informations $\endgroup$
    – jonny
    May 9, 2019 at 13:58

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