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
