Hello Peng, Please see the FAQ section for complete descriptions of file formats. These descriptions include information about compression or data loss.
For you other question, yes, wiggle data is compressed, resulting in minor data resolution loss and bedgraph is compressed without any data loss when extracted from the browser, as Hiram explained. Perhaps looking at the FAQ sections will be helpful to review as they contain all the details along with examples. http://genome.ucsc.edu/FAQ/ http://genome.ucsc.edu/FAQ/FAQformat http://genome.ucsc.edu/FAQ/FAQformat#format6 http://genome.ucsc.edu/goldenPath/help/wiggle.html http://genome.ucsc.edu/goldenPath/help/bedgraph.html Thanks! Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "genome" <[email protected]> > Cc: "Peng Yu" <[email protected]> > Sent: Wednesday, January 6, 2010 4:16:57 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] What is the difference between the wiggle format and > bedGraph format? > > Repost: > > > Subject: > > Re: [Genome] What is the difference between the wiggle format and > > bedGraph format? > > From: > > Peng Yu <[email protected]> > > Date: > > Sat, 19 Dec 2009 14:52:39 +1800 > > To: > > [email protected] > > > > To: > > [email protected] > > > > > > You haven't told me what 'original state' means. Could you let me > know? > > > > Do you mean bedGraph is a lossless format but wiggle is a lossy > format? > > > > On Sat, Dec 19, 2009 at 12:21 PM, Hiram Clawson <[email protected]> > wrote: > >> Good Morning: > >> > >> Wiggle tracks compress the data for storage and reduce > >> the precision of the input data values. The exact > >> data values can not be recovered from the compression > >> format. The bedGraph type of tracks store and use the > >> actual original data. Thus, the bedGraph tracks can > >> return the original data in the table browser. > >> > >> See also: > >> http://genome.ucsc.edu/goldenPath/help/wiggle.html > >> > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > >> http://genomewiki.ucsc.edu/index.php/Wiggle > >> > >> --Hiram > >> > >> Peng Yu wrote: > >>> I see the following description. > >>> > >>> http://genome.ucsc.edu/goldenPath/help/bedgraph.html > >>> > >>> "This track type is similar to the wiggle (WIG) format, but unlike > the > >>> wiggle format, data exported in the bedGraph format are preserved > in > >>> their original state." > >>> > >>> But it is not making sense to me what the difference between > wiggle > >>> and bedGraph is. What does 'original state' mean? Could the > >>> description on the webpage be revised to make it clearer? > > > > > > > ------------------------------------------------------------------------ > > > > Subject: > > confirm 7481677d3bd8feb0b87083ddf9cebae68fd60973 > > From: > > [email protected] > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
