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 -- Chih-yu Chen @ Mitchell Lab Cell and Systems Biology University of Toronto _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
