Hello Marcela, Yes, the information is stored with respected to the forward (+) strand. refNCBI is what is reported by dbSNP and refUCSC is what we find when we use the declared coordinates for independent base extraction. These are compared and inconsistencies are flagged with an "exception" (see the dbSNP track description for the list of exceptions and the table snpNNNExceptions for the data).
.nib is an older format used for genome sequence, this is actually based on the .2bit format now. http://genome.ucsc.edu/FAQ/FAQformat.html#format8 http://genome.ucsc.edu/FAQ/FAQformat.html#format7 I will pass this information on the development, perhaps the schema definition can be updated when the dbSNP track is next updated. Thanks! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 3/5/10 2:51 PM, Marcela Tello-Ruiz wrote: > > Hi, > > Is the refUCSC allele in the dbSNP tables always in the forward "+" > orientation relative to the reference genome sequence assembly? > > The description of this field reads "Reference genomic from nib lookup". > > Thanks, > > Marcela > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
