Hi Tim, There are a few choices for files approaching or exceeding 100MB:
1) Break the large files into smaller chunks (per chrom, smaller if needed). Good for annotation, where the data is wide (example: an attribute for every base) but not deep. If you are using .wig files, this is the choice to try first. 2) Compressed the individual reads into consensus sequences, then load results. Good for very deeply sequenced regions since these will be unviewable in the browser anyway past a certain depth of coverage. Compression does not have to be to a depth == 1. Depending on the experiment, the goal could be to remove redundancy to make variation more visible or to create summaries that weed out variation. 3) Consider creating a minimum browser install locally. You will still need to do 1 or 2 or both for large datasets (we do, here at UCSC, as well), but the data will not expire the way that custom tracks do on the main UCSC Browser. Meaning, if your data covers the entire genome, reloading per-chrom every few days could become a bother. The Sessions feature can help. Links: http://genomewiki.ucsc.edu/index.php/Category:Mirror_Site_FAQ http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html We hope one of these works out for you, Jennifer Jackson UCSC Genome Bioinformatics Group Tim Reddy wrote: > Hello, > > I've been having a recurring problem which in the past had been manageable, > but is getting worse with larger files arising from sequencing experiments. > When uploading large files to the genome browser as custom tracks (i.e. wig > files), I end up staring at a blank white screen, and the track appears to > be not loaded at all. I'm assuming the browser times out on long uploads > (~100MB, compressed), and do you know if there is an easy workaround for > this? > > Thanks, > Tim > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
