Hello Zohar, You can create a custom track of your genomic regions, and then select the custom track in the table browser with "output format: sequence" selected to get sequences for the regions you are interested in.
You will want to create a custom track in BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 You only need to use the first 3 fields in BED format. Be sure to subtract one from each of the start coordinates. For example, chr4:123456-123567 should become: chr4 123455 123567 Once you have your list of regions, either paste it or upload it as a custom track by hitting the "add custom tracks" button. Then go to the Table Browser and select your custom track and "sequence" as the output format. If you have any further questions, please feel free to write back to us at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/20/11 6:06 AM, Zohar Itzhaki wrote: > Hi, > > I have a list of mouse genomic regions (non-genes) which I want to retrieve > their sequence (e.g.: chr4:123456-123567) > I tried several tables in the table browser but none yielded any result. > How can I get the sequences? > > thanks, > > Zohar Barnett Itzhaki > Weizmann institute > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
