Hi, I downloaded wigToBigWig from this website
> http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ > > and put it inside my bin/, then run the sample wig file using the help at > the end of the above website, > > l...@bioinfo:~/Desktop$ wigToBigWig wigVarStepExample.gz hg18.chrom.sizes > zz.bw > bash: /home/litd/bin/wigToBigWig: cannot execute binary file > > > l...@bioinfo:~/Desktop$ ls -all ~/bin/wigToBigWig -rwxr-xr-x 1 litd litd 757119 2010-04-12 21:47 /home/litd/bin/wigToBigWig any help? > > Thanks! > > > > On Wed, Apr 7, 2010 at 3:36 PM, Hiram Clawson <[email protected]> wrote: > >> Do not use wig files. Use the bigWig files. >> wig files have size limits and are extremely inefficient >> compared to bigWig files. Use the bigWig files. >> >> >> Tiandao Li wrote: >> >>> How about wig files. not bigWig? still have size limits? >>> >>> On Wed, Apr 7, 2010 at 2:56 PM, Hiram Clawson <[email protected]> >>> wrote: >>> >>> No. bigWigs do not have size limits. They already have built-in >>>> zoom level calculations. Even when looking at an entire chromosome >>>> of data values, the amount of data transmitted is very small. >>>> >>>> Please note, Jim fixed a bug in the encoders yesterday. If you can >>>> get current CVS source from our public CVS server, you should have >>>> the fixed encoders. The bug was in some of the zoom level view point >>>> calculations. >>>> >>>> --Hiram >>>> >>>> >>>> Tiandao Li wrote: >>>> >>>> Great! If I upload big wig files on our web server, there is still size >>>>> limitation when I make a track points to them, right? >>>>> >>>>> On Wed, Apr 7, 2010 at 2:14 PM, Hiram Clawson <[email protected]> >>>>> wrote: >>>>> >>>>> You can have multiple tracks in one custom track submission. >>>>> >>>>>> Create a small file that is merely the track lines to each bigWig >>>>>> file. >>>>>> >>>>>> To submit the set of tracks, use the URL to this small file. >>>>>> Each track will be used. >>>>>> >>>>>> --Hiram >>>>>> >>>>>> >>>>>> Tiandao Li wrote: >>>>>> >>>>>> Good Afternoon Hiram, >>>>>> >>>>>>> Thanks for your quick response. Without local genome browser, I am >>>>>>> thinking >>>>>>> maybe I upload our wig files to our server, the problem is how to >>>>>>> create >>>>>>> multiple tracks in ONE URL and shared with others? The following >>>>>>> example >>>>>>> is >>>>>>> one URL for one track. >>>>>>> >>>>>>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Tiandao >>>>>>> >>>>>>> >>>>>>> On Wed, Apr 7, 2010 at 1:49 PM, Hiram Clawson <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>> 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
