Good Morning Rebecca: You can achieve the function you want with a minor change in your procedure. Instead of providing the gzipped wiggle ascii file for the track, use the wigToBigWig conversion program to construct a bigWig file type. On your track definition line, include a URL to that bigWig file with the bigDataUrl specification. This single track line is sufficient to show the track in the browser. The immense amount of data in the entire file is not required to be passed over to the genome browser to make the track appear. Only the bits that the user wants to see will be transferred as they are used. Since there is no massive transfer of data, there will be no time-outs in the genome browser. If your original wiggle data is in bedGraph format, use the bedGraphToBigWig conversion to bigWig.
You can do the same thing for bed format tracks. Use the bedToBigBed conversion program, and the same bigDataUrl reference from the track definition line. See also: http://bioinformatics.oxfordjournals.org/content/26/17/2204.short http://genome.ucsc.edu/goldenPath/help/bigWig.html http://genome.ucsc.edu/goldenPath/help/bigBed.html http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format --Hiram Rebecca Hudson wrote: > Hello, > > Our lab is trying to automate the process of creating links that our users > can use to view multiple custom wiggle tracks stored on our server in the > genome browser. > > We've created a program that builds a textfile that consists of track lines > and urls to gzipped wiggle track files on our server. > > This textfile is specified in the url after the browser line as > "hgct_customText=https://..."; > http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr8:128451376-128834335&hgct_customText=https://.../myTest.txt > > For larger files (that appear to cause the browser to time out) we have in > this aforementioned textfile a reference to another textfile that has urls to > each part of the wiggle track that is split into seperate gzipped pieces. > > We have encountered two major issues here: > 1. For all files tested that did not appear to time out the browser, this > error showed up: > "Expecting two words for variableStep data at line 11848720, found 1" > This is confusing because all of the variableStep lines have exactly two > words on them. > > > 2. All other files/data tested appeared to time out the Genome Browser. > If no error message is displayed; the browser reaches 100% loaded and > shows a blank page. > Is time-out what is happenning here? > > > What method (indirection, splitting?) do you reccomend for loading large > (100+ mb gzipped) wiggle tracks from a remote server? > Is there any reliable way to sidestep (what looks like) timeout? > > -Thanks _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
