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
