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 > > -- Daofeng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
