Hello Axel, If you want an easy way to convert coordinates from one assembly to another you may be interested in our liftover and convert tools.
The convert tool will take you directly from one assembly to another in the browser. You can get to the convert tool by clicking on "convert" in the top bar and selecting the target assembly (i.e. hg19) in the subsequent menu. If you would like to convert coordinates from one assembly to another (without necessarily opening up a browser at that location) you can use liftOver (http://genome.ucsc.edu/cgi-bin/hgLiftOver) accessible by clicking on the "utilities" link in the lefthand menu from the browser main page. Once you have converted your coordinates to hg19 you should be able to follow the same procedures you were using on hg18. You may also be interested in our getDna tool which returns the sequence for a given region. This can be accessed by clicking on "DNA" in the top bar in the browser. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/24/10 01:45, Weber, Axel wrote: > Hi UCSC Team, > I work with genomic array data and try to find out the best way to get > sequences from my array annotations. > For example I have got the information that in a DNA sample the region > Chr1:112,687,850-112,693,696 is deleted. > In my last Data set the annotation data was given with the hg18 assembly and > I found the "Extended DNA Case/Color Option" page the best way to deal with > my data. I just copied the coordinates of the region of interest in the > "position"-field and the result was the sequence of interest. That was > nice!!! > However, in our new array data set the data is given with the hg19 assembly > and here are the problems: > In the "Extended DNA Case/Color Option" I can not change between the > different assemblies so now I have to translate the sequence annotation data > but this feature does not work with every sequence and often results in error > messages. > Then I tried to go via the genome browser. The genome browser gives me a nice > overview either with the hg18 or hg19 assembly. But it does not show me the > sequence underlying the search and I can not find a button or link or track > leading to my sequence of the given coordinates (because here the track "your > sequence" like in the Blat-search when you use sequence-data as input, is > missing). > Is there a user friendly tool that makes a simple sequence output, when using > coordinates like Chr1:112,687,850-112,693,696 as input and let you change > between different assembly versions? > Thank you for your answer in advance, > Regards, > Axel Weber > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
