Hello Chih-yu, We can confirm. For this case, it not number of items but rather the combined stacked height that is triggering the dense view. The wider items result in less opportunities to share rows for a squish view. Zooming in is the only solution.
Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/23/10 2:43 PM, Julie Chih-yu Chen wrote: > Hi all, > > I have been uploading my own custom ChIP-seq custom tracks in bed format > to the genome browser and realized that in certain regions, squish or > full modes are automatically replaced by dense. > > The assembly I am using: Mouse July 2007 (NCBI37/mm9) Assembly and the > locations are listed below. > > ChIP-seq #1 > chr9:42,778,719-45,695,384 (total of 6263 tags) Squish not available > chr9:44,164,135-47,080,800 (total of 3418 tags) Squish available > > ChIP-seq #2 > chr9:42,778,719-45,695,384 (total of 8487 tags) Squish not available > chr9:44,164,135-47,080,800 (total of 6772 tags) Squish available > > ChIP-seq #3 > chr9:42,778,719-45,695,384 (total of 10880 tags) Squish available > chr9:44,164,135-47,080,800 (total of 10396 tags) Squish available > > I found an old post > (https://lists.soe.ucsc.edu/pipermail/genome/2005-October/008707.html) > stating that custom track results>1000 are automatically switched to > dense mode, and checked the source code to only to find out > "maxItemsInFullTrack" doesn't exist anymore. > But in my case, the number of tags doesn't seem to be the reason that > squish mode is replaced. (could it be the width of the tags?) > > Any help would be greatly appreciated. Thanks > > > Chih-yu > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
