Hi Mousheng, You can find a description of the fields for any table in the Genome Browser by selecting the table in the Table Browser and (http://genome.ucsc.edu/cgi-bin/hgTables) and hitting the "describe table schema" button, or by clicking the blue track name in the Genome Browser and then clicking the "View table schema" link.
In the case of 'dukeDnaseCd4Signal', you can make the following selections in the Table Browser: clade: mammal genome: human assembly: May 2004 group: regulation track: Duke Dnase Sig table: dukeDnaseCd4Signal To get this info from the Genome Browser, you can click on the supertrack name, "Duke DNaseI HS...", then on the track name "Duke DNase Sig". You will see the "View table schema" link on that page. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/18/08 07:55, mousheng xu wrote: > Dear Brooke, > > I've downloaded the files, but I do not think hgWiggle can do the > things I want and I am planning to parse the data file(s) myself. > Could you please tell me what each field in "dukeDnaseCd4Signal.txt" > is? An example line of this file is as follows: > > ---------------------------------------------------------------------------------------------------------- > 585 chr1 0 1024 chr1.1006546 1 1024 1030697103 > /gbdb/hg17/wib/dukeDnaseCd4Signal.wib -0.54671 0.34281 1024 > -463.838 224.368 > ---------------------------------------------------------------------------------------------------------- > > I am mainly interested in getting the Dnase signal level at each position. > > Thanks so much! > > -- Mousheng Xu > > On Fri, Nov 7, 2008 at 6:44 PM, Brooke Rhead <[EMAIL PROTECTED]> wrote: >> Hi Mousheng, >> >> One of my colleagues pointed out that there is a page on our genomewiki that >> describes how to get data values for wiggle tracks from the files that are >> already available via ftp: >> http://genomewiki.cse.ucsc.edu/index.php/Using_hgWiggle_without_a_database >> >> You will need the files: >> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/dukeDnaseCd4Signal.txt.gz >> ftp://hgdownload.cse.ucsc.edu/gbdb/hg17/wib/dukeDnaseCd4Signal.wib >> >> The "hgWiggle" tool is part of the Genome Browser source code, which is free >> for noncommercial use: >> http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads >> >> If you have further questions, please feel free to contact us again at >> [EMAIL PROTECTED] >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 11/07/08 12:50, mousheng xu wrote: >>> Dear Brooke, >>> >>> I have the "Duke DNase Sites" track already, but I do need the "Sig" >>> track. I would really appreciate it if you could make the "Sig" track >>> data available to me. One-score-per-base is fine with me. >>> >>> Thanks a lot! >>> >>> Sincerely, >>> >>> Mousheng Xu >>> >>> On Fri, Nov 7, 2008 at 3:30 PM, Brooke Rhead <[EMAIL PROTECTED]> wrote: >>>> Hello Mousheng, >>>> >>>> The "Duke DNase Sig" track in the hg17 database (dukeDnaseCd4Signal) was >>>> actually submitted to us as per-base scores. That is, the data is in >>>> fixed-step wiggle format, with 1-base steps. A description of the wiggle >>>> data format is here: >>>> http://genome.ucsc.edu/goldenPath/help/wiggle.html >>>> >>>> If you like, we can make the dukeDnaseCd4Signal wiggle file available to >>>> you. However, it will still be in a one-score-per-base format. >>>> >>>> You might be interested in using the "Duke DNase Sites" track instead of >>>> the "Duke DNase Sig" track. If not, and if you would still like the >>>> signal >>>> data in wiggle format, please let us know. >>>> >>>> -- >>>> Brooke Rhead >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> On 11/05/08 10:30, mousheng xu wrote: >>>>> Dear UCSC genome help, >>>>> >>>>> I am trying to get data in "dukeDnaseCd4Signal", but the data are >>>>> organized >>>>> in a very inefficient way -- signal is recorded for every base instead >>>>> of >>>>> subsequence. For instance, suppose chr1:100-200 has the same signal >>>>> level >>>>> -0.54, instead of giving chr1 100 200 -0.54 as one entry, >>>>> "dukeDnaseCd4Signal" gives 101 entries from position 100 to 200 with the >>>>> same value -0.54 like below >>>>> 100 -0.54 >>>>> 101 -0.54 >>>>> ... >>>>> 200 -0.54 >>>>> >>>>> The problem is that it unnecessarily takes enormous amount of space. >>>>> >>>>> Thanks a lot in advance! >>>>> >>>>> Sincerely, >>>>> >>>>> Mousheng Xu >>>>> >>>>> Research Fellow >>>>> Brigham & Women's Hospital >>>>> Harvard Medical School >>>>> 617-525-0739 >>>>> _______________________________________________ >>>>> Genome maillist - [email protected] >>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
