Hello, Performing the query using your method (region filter against the gold table) is pulling out the entire contig that contains the region. The region is acting as a filter - any overlap and the complete associated contigs are returned. Not what you want.
The "get DNA" method from within a genome browser session is one good way to get the sequence data for the range set by position. To use the table browser, create and upload a BED file of region(s). Then with that BED file loaded, select it in the Table browser, set output to sequence, and retrieve the sequence that way. http://genome.ucsc.edu/FAQ/FAQdownloads#download32 Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Bino John" <[email protected]> wrote: > From: "Bino John" <[email protected]> > To: "[email protected]" <[email protected]> > Sent: Tuesday, August 25, 2009 7:24:40 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] bug in UCSC table service? > > Hi, > I am using the settings as you see in the attached pdf. The settings > correspond to a query of size ~800 bases to be extracted from the > genome. However, I get a very long sequence much more than 800 in > length as the out put, and the output coordinates do not match the > coordinates I put in. > Please help -- How do we get the chromosomal sequences for a given > region in fasta format from the UCSC browser, if this bug can't b e > fixed quickly? > > Thanks > Bino > > Asst Prof > Univ. Pittsburgh > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
