Hello Jessica, We've had previous reports of similar problems with groups at McGill and the problem seems to have been at the McGill end. The easiest solution would be to save your custom tracks in a session, then distribute the session link rather than your local file link and this would get around the issue of having to upload your list of tracks every time someone is viewing them.
You can find more information about saving sessions here: http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html There is a limit on custom track size but it is fairly large and your track seems like it should be well below this limit. You can read more about the limit in this previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2007-April/013324.html As for your "Satellite" tracks question. You might trying using our table browser (http://genome.ucsc.edu/cgi-bin/hgTables). Select hg19, and: group: Variation and Repeats track: RepeatMasker table: rmsk Then click of "create" a filter, and input repClass does match Satellite, click submit. Then select BED as your output format. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Jessica Wasserscheid wrote: > Hi, > > We have had quite a hard time getting the browser to work efficiently in > the past 2 weeks. We have a large publicly available custom tracks file, > that is loaded regularly (and has been for the past few years) and even > though the file has gotten a little bigger recently, the browser seems > abnormally slow. > > Is there an exceptionnal amount of users recently that would slow down > the access ? or a temporary problem on your side ? > > The file of custom tracks is available here (to be loaded on hg19): > http://www.genomequebec.mcgill.ca/compgen/submit_db/bed/vervet_vs_humanhg19_custom_tracks.txt > > We have an equivalent file for the genomes of rhesus and chimp, but it > seems much faster to work with these. > http://www.genomequebec.mcgill.ca/compgen/submit_db/bed/vervet_vs_rhesus_custom_tracks.txt > http://www.genomequebec.mcgill.ca/compgen/submit_db/bed/vervet_vs_chimp_custom_tracks.txt > (one of the tracks in the human file concerns some fish experiments, and > they are recent add-ons, are these tracks "heavier" because they access > an html page ?) > > Is the problem on our side ? Does the fact that 2 or more computers on > our server try to access the browser at the same time, with the same > public custom track file, cause the problem ? > > I personnally had trouble getting the pages to finish loading (it would > time out after a while) or zooming out after I locally loaded an extra > bigBed file. It would sporadically work. I had to remove the custom > tracks mentionned above to get it to work, but it's still not as smooth > as it used to be. > Is there a size limit for the custom tracks we should be able to load ? > Could that bigBed file cause the slowlyness problem for the other users > in my group, or should our computers be completely independent when it > comes to accessing the UCSC browser ? > > My other question is more straight forward : I am trying to extract the > subset of "Satellite" tracks from the RepeatMasker bed file for the > genomes of human and rhesus, but since they belong to different classes, > I have no way to know if a name is part of the class Satellite. I > manually extracted some of them, but it would be greatly appreciated if > you can send me the isolated subsets of satellite tracks for hg19 and > rheMac2. > > Thanks a lot for your help ! > > Jessica > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
