Hi Julie, If you specify strand in a bed custom track (at least a 6 column bed file (i.e. BED6)), the table browser returns the sequence from the strand specified in the bed track. If you do not specify the strand, it is assumed to be the positive strand.
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group ----- Original Message ----- From: "Julie Ahringer" <[email protected]> To: [email protected] Sent: Friday, August 20, 2010 9:03:33 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] Retrieving DNA corresponding to list of coordinates If I upload a narrowbed format file that has strand information, and then retrieve sequence corresponding to those coordinates using the Table browser, will it return sequence on the correct strand? Or will it just give me the positive strand? If I leave strand info out (e.g, just use a bed file), then do I get the positive strand? Thanks, Julie -- ___________________________________ Dr. Julie Ahringer The Gurdon Institute University of Cambridge Tennis Court Road Cambridge CB2 1QN UK phone +44 1223 334142 (Office) 334144 (Lab) fax +44 1223 334089 NOTE NEW EMAIL ADDRESS: [email protected] http://www.gurdon.cam.ac.uk/~ahringerlab/ ___________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
