How To Separate Transposon-Derived Repeats From Other Repeats

Question

[biorepine]

Hi guys, I downloaded hg19 and mm9 repeat masker repeats from UCSC table browser. Do you know how to separate transposon-derived repeats from other repeats ? Thanx in advance!

[KCC]

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'.

Answer 1

[PoGibas]

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.