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
