How To Separate Transposon-Derived Repeats From Other Repeats
1 answer
Repbase contains repeats subdivided according to class.
1. Filter by taxon (mammalia, mus musculus, homo sapiens);
2. Filter by repeat class (Transposable elements (DNA, LTR, non-LTR), simple repeat, pseudogene);
3. Download (you have to register first);
4. Grep out lines from the repeat masker file according to downloaded list.
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In the file provided by the table browser, aren't there columns like "repName", "repClass" and "repFamily"? I think these have the information you want. Although, I don't think anything is specifically labeled 'transposon'.