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Old 03-05-2013, 01:43 AM   #1
dpolychr
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Default Noncoding human genome (hg19)

Hi all,

I would like to download in BED the coordinates of the noncoding human genome. I was thinking to exclude Refseq genes and repetitive elements and then take what is left but how can I do that?Only the .fa files are available and I need the chromosomal coordinates

Any suggestions would be really helpful
Dimitris
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Old 03-05-2013, 02:56 PM   #2
swbarnes2
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You could try making a .bed file of the full genome, and maybe intersectBed -v from BEDTools would return what you wanted.
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Old 03-05-2013, 06:24 PM   #3
dvanic
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UCSC table browser. If you go to UCSC and click on tables, and then use all regions that have no overlap with refseq as a custom track, followed by further intersecting that track to have no overlap with repeat masker you will get what you want in a matter of minutes, no command line required.
Hope this helps
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Old 03-07-2013, 01:42 PM   #4
dpolychr
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thank you all for your help
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