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Old 02-05-2014, 02:52 AM   #1
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Default 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
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Old 02-05-2014, 03:17 AM   #2
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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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Old 02-05-2014, 03:30 AM   #3
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Quote:
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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Old 02-05-2014, 03:38 AM   #4
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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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Old 02-05-2014, 06:17 AM   #5
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i can't seem to find it in the iGenomes neither
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Old 02-05-2014, 06:39 AM   #6
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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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Old 02-11-2014, 01:48 AM   #7
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Quote:
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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Old 02-11-2014, 02:16 AM   #8
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Just let me know when you've finished downloading it so I can clear some space on dropbox.
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gff, gtf, line/sine/erv, repeat

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