Thanks Hiram, I went through your link, but it still doesn't answer my question, it is still focused on the format. Let me ask the question again, in a wiggle file, in a given position of the genome, what does it mean to have a value of 3000 and what does it mean to have a value of 0.5 in another position of the genome for a track let's say representing a histone modification mark.?
Rad On Jan 14, 2012, at 11:52 PM, Hiram Clawson <[email protected]> wrote: > These data file formats allow an experimenter to display data values at base > positions. > The data values an experiment generates are a decision made by the > experiment. The files are merely > the delivery mechanism to get the data values into the genome browser. The > data values have > no meaning without reference to the experiment that produced them. When you > are viewing > one of these data tracks the data values are graphed along the genome at > their respective > positions. To discover the meaning behind the graph, examine the description > page > for the track to see what the experiment is graphing. See also: > > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > > --Hiram > > ----- Original Message ----- > From: "Radhouane Aniba" <[email protected]> > To: "Genome List" <[email protected]> > Sent: Saturday, January 14, 2012 8:25:37 PM > Subject: [Genome] Wig, bigwig, bedgraph, in depth documentation > > Hello everyone, > > All of us, at least people working on NGS data analysis, are familiar with > these three data types, and we are refering to UCSC documentation to > understand their content and meaning. That's nice, but still there is some > black boxes not necessary clear especially these questions : > > how comes that these files generated for the same experiment by different > programs, create different values and different distribution > a question that is more related to these programs now, how are these files > created from reads alignments ? What algorithm is behind these files ? > documentation on the format are clear enough, but significance and meaning of > the scores inside each file are not explained, what are these values > referring to ? > look at this sentence from UCSC " The BedGraph format allows display of > continuous-valued data in track format. This display type is useful for > probability scores and transcriptome data" : probability score ? Of what ? > How ? > I hope i am not merging a lot of questions in a single post, they are all > related and i think it is worth mentionning them in block so that we can > discuss them in the same time. > > Thanks for all. > > Rad > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
