MULE appeared in RepeatModeler xxx-families.fa, but no MULE were annotated by RepeatMasker - Githubissues

Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

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MULE appeared in RepeatModeler xxx-families.fa, but no MULE were annotated by RepeatMasker #175

Closed leon945945 closed 2 years ago

leon945945 commented 2 years ago

Hi, I've successfully run RepeatModeler and RepeatMasker to mask the genome I used, but I was confused when I checked the mask results:

There are MULE DNA transposons in xxx-families.fa, like these:

>rnd-1_family-84#DNA/MULE-MuDR ( RepeatScout Family Size = 298, Final Multiple Alignment Size = 100, Localized to 10 out of 10 contigs ) >rnd-1_family-178#DNA/MULE-MuDR ( RepeatScout Family Size = 154, Final Multiple Alignment Size = 100, Localized to 10 out of 10 contigs )
I feed the xxx-families.fa to RepeatMasker, but no MULE were annotated by RepeatMasker as indicated by x.tbl file: DNA transposons 44194 17374798 bp 5.16 % hobo-Activator 18412 6214929 bp 1.85 % Tc1-IS630-Pogo 3072 942369 bp 0.28 % En-Spm 0 0 bp 0.00 % MuDR-IS905 0 0 bp 0.00 % PiggyBac 0 0 bp 0.00 % Tourist/Harbinger 6025 2190999 bp 0.65 % Other (Mirage, 0 0 bp 0.00 % P-element, Transib)

As you can see, the MuDR-IS905 type was 0 bp, it confused me, could you please answer my confusion?

rmhubley commented 2 years ago

The MuDR classification name has changed recently and the RepeatMasker code that generates the table was outdated. I have fixed this in 4.1.3-p1. Another suggestion would be to use the util/buildSummar.pl script to generate a summary table and a full accounting for each family found in the *.out files.