[giampe]

hello everyone,
I'm posting my question here since you are talking about repeat element!
My question is :where I can find a complete and recent database of transposable elements of Vitis vinifera (Grape) and download it?
thanks.

[Simon Anders]

Such a long thread on how to use repeatmasker, but nobody has answered the actual question:

For the RNA seq data, I want to filter out reads from house keeping RNA, is it reasonable to use repeatmask as the filter？

No, it is not reasonable.


liuxq, maybe you could tell us what you actually want to do. I don't know what you mean by "house keeping RNA", but I cannot fathom what it may have to do with repeat regions.

What lh3 was hinting at: Many users are worried that an aligner might get confused by repeat regions and want to remove them from the reference. This is unnecessary, aligners do fine with them and indicate if a read maps to multiple locations, allowing to filter afterwards if needed.