Tandem repeats in gff/gtf format

[roll]

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

[dpryan]

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

[roll]

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

[dpryan]

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.

[roll]

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

[dpryan]

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).

[roll]

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

[dpryan]

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