Hi Yan, The best way to do this is to first make a custom track with your regions (there's a add custom tracks button in the Table Browser). For info on making a custom track see: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks.
Now in the Table Browser select 'group: Custom Tracks', 'track: <your custom tracl>', make sure region is set to genome, and then select sequence for the output. This will get the sequence for just the regions you want. (The reason the method you were trying to do wasn't working is that you were getting output of sequence of only where your pasted list of regions /overlapped/ with whatever track's regions that was selected in the browser.) Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 2/10/12 7:42 PM, Wu, Yanhong, Ph.D. wrote: > I am very confused by the Table Browser sequence output. I have a list of > regions (~ 500bp) that I like to get the fasta sequence output, instead of > getting the sequence from the "DNA" tab, I thought Table Browser may be a > better way. I entered a list of regions in the table browser, selected > "sequece" as output, however, the sequences I got is not what I entered and > there are more regions that I entered in. I am not sure why, can you explain > what is included in the sequnce output from table browser? thanks. > Yan > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
