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
