Hi Reza, Are you looking for the data in the Conserved Elements tracks on the hg19 or hg18 assembly? If so, you can get this data from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) in BED format. Select the hg19 or hg18 assembly in the Table Browser, and then select:
group: Comparative Genomics track: Conservation table: Vertebrate El (phastConsElements46way) (alternatively select Mammal El or Primate El, depending on what data you want) region: select "genome" or else select "position" and enter a chromosome name (e.g. "chr1") output format: BED - Browser Extensible Data output file: enter a filename here if you would like to download the results to a file rather than see them in your internet browser Finally, hit "get output." If you are totally unfamiliar with the UCSC Genome Browser, there are some good tutorials here that you might want to see: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml The Table Browser tutorial might be especially helpful: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 1/27/12 12:56 PM, reza sodaie wrote: > how can I download element.bed of a chromosome? > > On Sat, Jan 28, 2012 at 12:22 AM, reza sodaie<[email protected]> wrote: > >> 530 Access Denied - You have too many open sessions already! >> what is this error? I wanted to download some multiz alignment from ftp >> server, and I used anonymous as user and my email address. >> >> >> On Fri, Jan 27, 2012 at 11:22 PM, reza sodaie<[email protected]>wrote: >> >>> Thank you very much. >>> I need someone's cooperation or supervision in finding some accelerated >>> region in genome using RPHAST, may you? or do you know anyone? >>> >>> >>> >>> On Fri, Jan 27, 2012 at 10:22 PM, Hiram Clawson<[email protected]>wrote: >>> >>>> You are referring to the resources that are used to >>>> construct the conservation track. You can read all about >>>> the conservation track: >>>> >>>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way >>>> >>>> Your reference to .GP files are genePred files: >>>> >>>> http://genome.ucsc.edu/FAQ/FAQformat.html#format9 >>>> >>>> There are many gene tracks and tables. You decide what genes >>>> you want to use. You can fetch them from the table browser or >>>> the download server. There are several "elements" tables in >>>> the 46-way conservation track. Decide on what you want to use. >>>> Obtain it from the table browser or the download server. >>>> >>>> You would want to become familiar with the genome browser: >>>> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html >>>> And the table browser: >>>> http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html >>>> >>>> --Hiram >>>> >>>> ----- Original Message ----- >>>> From: "reza sodaie" >>>> To: "Hiram Clawson" >>>> Sent: Friday, January 27, 2012 10:41:07 AM >>>> Subject: Re: [Genome] GP file >>>> >>>> I have encountered this kind of file in these vignettes. >>>> and is there any element.bed file? >>>> >>> >>> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
