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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.
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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.Leave a comment:
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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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