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Old 01-18-2011, 04:44 PM   #1
trickytank
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Location: Melbourne

Join Date: Dec 2010
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Default SpliceMap Gene annotations file for hg19

Hello,

I'm using SpliceMap to identify novel exon junctions, but want to do all this on hg19. SpliceMap includes gene annotations for hg18 in example download, but not for hg19.

Is there a good way to get the annotations for Ensembl, RefSeq and knowngene for hg19 that will work with SpliceMap? (Just like the annotations in the example, except for being for the hg19 build.)

I can get the RefSeq ones working from the refFlat.txt file from UCSC, but haven't had any success with .bed annotation files I've tried to use that were downloaded from the UCSC table browser. (SpliceMap appears to mark almost all junctions as novel but when viewed in the UCSC browser they look well annotated.)

Thanks for your help,
Rick
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