This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Find Coordinates For Transposon

I need transposon (Alu, L1, LTR, SVA, ERV) coordinates in BED format. Seems they are labeled at UCSC genome browser, but I need the file. Can I download the file or the coordinates from somewhere at UCSC website/

thx

coordinates
• 4,646 views • link
updated by Casey Bergman Casey Bergman • written by Bioscientist Bioscientist

Can you link to an example at UCSC so we can see which track it belongs to?

• 0 views • link
written by Neilfws Neilfws

1 answer

You can get this data from the UCSC table browser. Just click this link, select BED from the "output format" dropdown menu and click "get output" and then "get BED" on the next page.

• 0 views • link
written by Casey Bergman Casey Bergman

Yes, but this is program generated output. Can I find list of all transposable elements (for instance in hg19) which was treated manually and has better accurance? Thanks:)

• 2 views • link
written by Biomonika (Noolean) Biomonika (Noolean)

Log in to answer this question.

More posts like this