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
