David, If you upload your BED file as bed6 custom track, then the Table Browser's sequence output should honor the strand.
If you're going to do this many times, you could use twoBitToFa-BED with the same BED6 file, and could script it instead of using the website directly. This also might have some useful tips: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32 Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 7/18/11 2:33 PM, Managadze, David (NIH/NLM/NCBI) [F] wrote: > Could you please tell me which group,track and table should I use to get the > genomic sequences assembly EXACTLY corresponding to the particular > region+strand I ask. > > I would like to get these chromosome sequences based on my BED file, i.e. I > have many of them and want to do it in a batch mode. > > In other words, I want to do exactly the same as clicking "get DNA" on this > page: > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=203298703&o=173958904&g=getDna&i=mixed&c=chr1&l=173958904&r=174018184&db=hg19&hgsid=203298703 > would give. > (This is accessible from the menubar of Genome Browser, the link "DNA", but > is obviously for just one region, not for batch mode :) ) > > I tried to do this via Table Browser's different groups/tables with no > success. > (Genes and Gene predicion tracks, Mapping and sequencing tracks etc)/ > > As a result I got sequences of different regions (at least the returned > coordinates were different). > > Another problem is that Table browser does not "honor" strand if I want to > define regions; i.e. it does not accept the strand (only 3 or 4-field BED) > which means that I have to keep track of the strands of every region and > reverse-complement the sequence if strand was "-". > > Thank you in advance, > Best, > > David > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
