Finding position of transposones in human genome.

Question

[SP]

Hello,

I am searching position of different transposones on ENSEMBL Human genome. I have chip-seq data which I have aligned to transposone reference. So I have tag count per transposone. To further analyse my data I want the position of these transposones on genome.

Is there a database where respective positions of transposones are given? or is there any other way to find it out?

Thanks

[PoGibas]

What is your question?

[SP]

Sorry, I was not clear enough. How to find position of transposones on genome?

Answer 1

[PoGibas]

RepeatMasker annotation in UCSC genome browser contains this information. Download dataset and filter filter out non-transposone repeats.

[SP]

Thanks for the suggestion, I have found the annotations. Can I compare the chromosome positions of on UCSC to ENSEMBL?

[PoGibas]

If it is the same genome build, then you can. If not, just use liftover to convert between builds.