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  • Tandem repeats in gff/gtf format

    Hi,

    I am trying to find tandem repeats (mainly SINE,LINE, ERV) position in gff/gtf format. I don't know if such files exist but i will be gratefull if you know such databases that I can download the above files.

    Thanks

  • #2
    If you're species of interest is available via UCSC, then you can get the RepeatMasker track in GTF format via the table browser.

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    • #3
      Originally posted by dpryan View Post
      If you're species of interest is available via UCSC, then you can get the RepeatMasker track in GTF format via the table browser.
      thanks. i tried and it keeps giving me the following error

      Can't start query:
      describe rmsk

      ---------------------------------------------------------------------------
      ---------------------------------------------------------------------------
      mySQL error 1146: Table 'mm9.rmsk' doesn't exist

      it seems to work for mm10 though

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      • #4
        Check iGenomes to see if that comes with the indexes for mm9 (it might). If not, let me know and I'll see if I can upload my local copy of the mm9 repeatmasker output in GTF format somewhere for you.

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        • #5
          i can't seem to find it in the iGenomes neither

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          • #6
            Here you go. I don't recall if that's one I made with repeatmasker or if it's one I downloaded, though the results should be close to identical in each case (I would have used a more recent version of the repeat database than used by UCSC).

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            • #7
              Originally posted by dpryan View Post
              Here you go. I don't recall if that's one I made with repeatmasker or if it's one I downloaded, though the results should be close to identical in each case (I would have used a more recent version of the repeat database than used by UCSC).
              thank you dpryan

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              • #8
                Just let me know when you've finished downloading it so I can clear some space on dropbox.

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