Hello, Many of these datasets can be quite large, as you noticed. The most immediate remedy is to break up the file into smaller pieces (by chromosome, smaller if necessary) and load individually. Use our Sessions feature to increase the amount of time the custom data will stay loaded (although we cannot guarantee this ... please keep backup copies of all data/settings). http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html
This has been an issue that many internal and external users have encountered and we actively working on better method to load larger datasets. We release a new code base version approximately every two weeks and post the highlights of changes/additions to the Genome-announce mailing list. That would be the best place to find out about new tools, including those related to custom tracks. http://genome.ucsc.edu/contacts.html We hope this advice is helpful to you, Jennifer Jackson UCSC Genome Bioinformatics Group Daniel Campbell wrote: > I'm having a problem displaying some Custom Tracks based on data from the > following paper: > > Wei G, Wei L, Zhu J, Zang C et al. Global mapping of H3K4me3 and H3K27me3 > reveals specificity and plasticity in lineage fate determination of > differentiating CD4+ T cells. Immunity 2009 Jan;30(1):155-67. > > The authors deposited a several data sets as .bed files into the GEO database > at NCBI. IF the files are small (~20-50Mb), I have not problem loading them > and visualizing them in the genome browser. However, the bigger files (up to > 150Mb) will not load. The web browser (either Internet Explorer or Firefox) > just keeps thinking until it quits. Are there any tricks for uploading and > visualizing large files as custom tracks in the UCSC browser. Thanks in > advance for any help or suggestions provided. > > -Daniel > > Daniel J Campbell, PhD > Associate Member > Benaroya Research Institute > [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
