Questions #1-3 retracted. I realized that if I convert UCSC's reported intervals from 0-based to 1-based coordinates, I obtain accurate, LEFT-CLOSED, RIGHT-OPEN intervals that conform to BED specification.
Cheers! Tim On Jul 15, 2009, at 10:46 AM, Tim Yu wrote: > Can someone explain to me the standards for denoting intervals in > UCSC BED format? I'm struggling with what seem to me to be > inconsistencies: > > 1. From the UCSC FAQ describing the BED format > (http://genome.ucsc.edu/FAQ/FAQformat#format1 > ), it sounds as if intervals are LEFT-CLOSED/RIGHT-OPEN. For > instance, a feature spanning bases 0-99 (inclusively) is denoted > chromStart 0, chromEnd 100. > "The first three required BED fields are: > > chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or > scaffold (e.g. scaffold10671). > chromStart - The starting position of the feature in the chromosome > or scaffold. The first base in a chromosome is numbered 0. > chromEnd - The ending position of the feature in the chromosome or > scaffold. The chromEnd base is not included in the display of the > feature. For example, the first 100 bases of a chromosome are > defined as chromStart=0, chromEnd=100, and span the bases numbered > 0-99." > 2. On the other hand when I download lists of exon start/stop > positions from hg18>UCSC Genes>knownGene>Exons in BED format, the > resulting intervals appear to be the opposite: LEFT-OPEN, RIGHT- > CLOSED. Here is a representative entry. Looking at the browser, the > actual exon encompasses bases 2476-2584: > chr1 2475 2584 uc001aaa.2_exon_1_0_chr1_2476_f 0 + > > 3. I wondered if it was a strand issue, but here is an entry on the > - strand, which is also LEFT-OPEN, RIGHT-CLOSED. > chr1 4832 4901 uc001aab.2_exon_1_0_chr1_4833_r 0 - > > 4. Finally, what convention does dbSNP use? Many seem to use closed > interval notation, eg rs5887673, listed at chr7:133624600-133624603. > > Thanks for any help. > > Tim _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
