Good Morning Tiandao: As you have noticed on: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
the bigWig is the recommended alternative. You do not need to use the wiggle ascii format. You want to run the wigToBigWig encoder and use the bigWig file format. That will allow you to use any size of file and you do not need to have a local genome browser installation. Use the bigWig format to avoid these size limitations. --Hiram Tiandao Li wrote: > Hi, > > I loaded one of our tracks (wig) onto UCSC genome browser. The error msg is > > *File 'PolII_eland_sorted_pos4.wig.gz' - track load error (track > name='ct_PolIIIndex4_7269'): > wibSizeLimit of 300000000 has been exceeded; you must use bedGraph's for > files with more data points > > *the file size is 18.2M, compressed gz is 5.8 MB, wc shows only 1691995 > lines. We loaded a wig gz file of 13.5 MB to UCSC browser without any > problem. > > I found the following info > > https://lists.soe.ucsc.edu/pipermail/genome/2009-October/020211.html > > I can change wig to bigWig, then load to UCSC website. > > I have some questions about wig size limit. > 1. the size limit refers to file original size, or compressed size, or lines > of file, or something else... > 2. If I install genome browser locally, there will not size limit for wig > file size, right? > 3. since my variableStep wig data is not quite dense overall, which format > is my best choice to load to genome browser, wig, bedGraph, bigWig, or > bigBed..? I am not a fan of binary files. > > http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format > > *Caution for sparse variableStep data* > The wiggle format was designed for quickly displaying data that is quite > dense. The variableStep format, in particular, becomes very inefficient when > there are only a few data points per 1,024 bases. If variableStep data > points (*i.e.*, chromStarts) are greater than about 100 bases apart, it is > advisable to use > BedGraph<http://genome.ucsc.edu/goldenPath/help/bedgraph.html>format. > > Thanks, > > Tiandao _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
