Hi Eduardo, For information about the ENCODE tracks beyond what you can find in the description page, please refer to the References section or contact the submitting laboratory (in the "Credits" section, see "contact:").
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/26/11 1:50 PM, Eduardo Gade Gusmão wrote: > Hello, > > I am not sure about who I should send this email to. Please let me know if > you are not the one supposed to answer these questions. If that's the case, > can you provide me the correct contact? > > I have two questions concerning the data from the DUKE experiment on Open > Chromatin available here: > http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromDnase > > 1 - In the "Display Conventions and Configuration" section in the bottom of > the site you say: > "Peaks and signals displayed in this track are the results of pooled > replicates." > > Where can I find the explanation of how this "pooling" was made? > > 2 - In the "Methods" section you say that the wiggles were generated using > the following command: > "fseq -l 600 -v -f 0 -b<bff files> -p<iff files> aligments.bed" > "Where the (bff files) are the background files based on alignability, the > (iff files) are the background files based on the Input experiments, and > alignments.bed are a bed file of filtered sequence alignments." > > What exactly are those bff and iff files? Where the actual alignment files > from the replicates used in this command since all the files are background? > There is any text/article that explains how this procedure was made? > > And what exactly is a filtered sequence alignment? > > To summarize all these issues: I want to replicate, in part, the wig/bigWig > generation from the bam/bam.bai files. There is any text/article that > explains how this task was done in more details? > > Thank you very much in advance! > ________________________________________________________________ > Eduardo Gade Gusmão > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
