One slight correction. If you are talking about using bigWig and bigBed files locally in a mirror installation, yes, they can be used as files locally and do not need to be URL resources.
The 'loading' of the file into the database is merely a one column entry into its tableName database table, for example: hgsql hg19 -e 'drop table if exists myLocalBigWig; \ create table myLocalBigWig (fileName varchar(255) not null); \ insert into myLocalBigWig values ("/gbdb/hg19/bbi/myLocalBigWig.bw");' The entry in the trackDb.ra file is just like a 'type wig min max' except it is now 'type bigWig min max' Note comments in the hg/makeDb/trackDb/README file about this. --Hiram Hiram Clawson wrote: > bigWig (and bigBed) files must be URL resources. They are not files to be > passed whole to our server. The benefit is the saving in transport > time. Only the bits that are needed for a particular view in > the browser are transported as needed. The bits transferred accumulate > in a cache at our end so that subsequence views of the same data > require no transfer at all. > > --Hiram > > David Hoover wrote: >> While we're talking about this, is it possible to upload a bigWig file >> into custom tracks using the same mechanism as a wig file, or must the >> file be on a remote server and accessed through a URL? >> >> Hiram Clawson wrote: >>> Good Morning David: >>> >>> Are you talking about the database contents of >>> the wiggle data, or the source ascii files that >>> are given to wigEncode ? >>> >>> If they are just the source ascii files, they >>> can all go together with 'cat': >>> $ cat files*.wig > result.wig >>> >>> If they have custom track and browser lines in them: >>> $ egrep -v "^track|^browser" files*.wig > result.wig >>> >>> Or, all these can be sent into wigEncode: >>> $ egrep -v "^track|^browser" files*.wig | wigEncode stdin result.wig >>> result.wib >>> >>> We now try to distinguish source files with the suffix: >>> .wigFixed or .wigVar >>> for fixedStep or variableStep wiggle ascii data. >>> >>> You may also be interested in the more efficient >>> encoding mechanism of wigToBigWig and the resulting .bw >>> file which can be a URL resource. See also: >>> http://genome.ucsc.edu/goldenPath/help/bigWig.html >>> This encoder works for bedGraph file types too and is >>> much more efficient: >>> http://genome.ucsc.edu/goldenPath/help/bedgraph.html >>> >>> --Hiram >>> >>> David Hoover wrote: >>>> I have multiple .wig files, one for each chromosome. Is there source >>>> code for an executable to concatenate the .wig files into a single >>>> .wig file? >>>> >>>> David Hoover >>>> Helix Systems Staff >>>> http://helix.nih.gov > > _______________________________________________ > Genome maillist - Genome@lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome