Hi Daofeng, No, UCSC does not generate these bigWig files. Please contact the data provider for more information.
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 11/14/11 12:24 PM, Daofeng Li wrote: > Hi Vanessa, > > Thanks for your response. > However, i didn't found any descriptions about how the bigWig files were > generated from the link you provided. > I also have contacts with some data centers, it seems they only provide > .bam or .qseq files. > I think that the bigWig files were generated by UCSC group? am i wrong? > > Thanks again. > > Best wishes. > > On Mon, Nov 14, 2011 at 1:41 PM, Vanessa Kirkup Swing > <[email protected]>wrote: > >> Hi Daofeng, >> >> We recommend that you look at the track description page for each track >> that you are interested in to get the information about how the data was >> generated. To get to the description page from the downloads page ( >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/) >> there is a link in the README that gives a filterable list of these files: >> >> http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone >> >> Click on the that link. In the upper right hand corner there is a >> "Description" link that should contain the information that you are looking >> for. If the description page doesn't answer the questions you have, we >> recommend that you contact the lab that contributed the data. The contact >> information for the lab is also provided on the Description Page. >> >> If you have further questions, please contact the mailing list: >> [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> >> ---------- Forwarded message ---------- >> From: Daofeng Li<[email protected]> >> Date: Thu, Nov 10, 2011 at 8:46 PM >> Subject: [Genome] Question about the encode data >> To: [email protected] >> >> >> Dear list, >> >> I am not sure whether this mailing list was the right place i ask this >> question, sorry if i am wrong. >> I want to ask the bigWig files for those bam files in the encode data (for >> example: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/ >> , >> there was wgEncodeBroadHistoneGm12878ControlStdSig.bigWig< >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig >>> , >> and wgEncodeBroadHistoneGm12878ControlStdAlnRep1.bam< >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdAlnRep1.bam >> , wgEncodeBroadHistoneGm12878ControlStdAlnRep2.bam< >> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/wgEncodeBroadHistoneGm12878ControlStdAlnRep2.bam >> ) >> What i want to ask is that how do you generate those bigWig files when >> replicates exists? >> Do you use the sum of hits of reads from two bam files? or use >> the average value? or else? >> >> Appreciated for any response. >> >> Best wishes. >> -- >> Daofeng >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
