Hi Matteo, While we don't yet have the SNP 134 data available on our main site, we do have the track currently in development. Since the track/data are available on our genome-preview site, you can download the data to use as input for your liftOver. Please note: Genome-preview (http://genome-preview.ucsc.edu/) allows users to preview tracks/data before they have been through our quality assurance process. Because genome-preview contains pre-release data, please use discretion when downloading and viewing data from genome-preview as it may still be undergoing changes and improvements.
Here is a link to the track controls/description of the preview of the All SNPs(134) track: http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp134 Here is the preview of the data that you can use as your input to the liftOver: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/database/ Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 9/30/11 10:15 AM, Katrina Learned wrote: > Hi Matteo, > > First, I would suggest double-checking to make sure your bed file is > correctly formatted. Here is detailed information about the bed format: > http://genome.ucsc.edu/FAQ/FAQformat.html#format1. For example, make > sure your chromosome fields are formatted as chr1 rather than chrom1. > > Second, if you are trying to lift specific regions of dbSNP134 data to > hg18, then you might not be getting mappings because there are some > regions of hg19 not in hg18. To see diffs between the two assemblies, > you can use these tracks: > > on hg18 > Hg19 Diff: Contigs dropped or changed from NCBI build 36(hg18) to > GRCh37(hg19) > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=hg18ContigDiff > > on hg19 > Hg18 Diff: Contigs new to GRCh37/(hg19), not carried forward from NCBI > build 36(hg18) > http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hg19ContigDiff > > If you're still having trouble, please paste a sample section of your > bed file in an email reply to the list so we can further troubleshoot > the issue. > > Thanks! > > Katrina Learned > UCSC Genome Bioinformatics Group > > On 9/30/11 2:12 AM, Matteo D'antonio wrote: >> Hello, >> I am finding problems in converting the coordinates of dbSNP134 from hg19 to >> hg18. I have downloaded the coordinates from NCBI and I converted them into a >> BED file. I use the original hg19ToHg18.over.chain. >> liftOver snps.hg19.bed hg19ToHg18.over.chain snps.hg18.bed unMapped >> The output file is always empty and all the coordinates have the tag >> "#Deleted >> in new" in unMapped. >> I have the same problem with a list of human genes in hg18 that I tried to >> map >> to hg19. >> >> Can someone help? >> Thanks! >> >> Matteo >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
