Good Evning Peng: In your second usage example, you are missing the specification of the database. Evidently, even when using the chromSizes file, it still needs a specification of the database. This is an error in our program that we need to fix. Thank you for bringing this to our attention. Try it like this:
sort t.bed | bedItemOverlapCount mm9 -chromSize=mm9.chrom.sizes stdin And, instead of using wigEncode on the output of this program, I would recommend using bedGraphToBigWig and using the resulting bigWig file. This is much more efficient than using wigEncode. The same options in a custom track for wiggle types of tracks are valid for bigWig tracks. See also: http://genome.ucsc.edu/goldenPath/help/wiggle.html http://genome.ucsc.edu/goldenPath/help/bigWig.html As an aside, you can set up your system to use the public MySQL server so you do not need to fetch the chrom.sizes file. Add a file to your home directory called: $HOME/.hg.conf set its permissions to 600: chmod 600 .hg.conf and insert the following three lines: db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password See also: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 This will enable all kent source utilities to use the public MySQL server. --Hiram >> On 4/5/10 12:56 PM, Peng Yu wrote: >>> I see the example on bedItemOverlapCount. >>> >>> https://lists.soe.ucsc.edu/pipermail/genome/2008-September/017062.html >>> >>> But I get the following error, when I try to run the program. >>> >>> $ cat t.bed >>> chr1 32000 34000 >>> chr1 33000 35000 >>> chr1 33000 35000 >>> $ sort -k1,1 -k2,2n t.bed | bedItemOverlapCount mm9 stdin >>> Couldn't open<home>/.hg.conf , No such file or directory >>> >>> I also tried the following two commands, the last statement of which >>> doesn't generated any file or screen output. >>> >>> $ fetchChromSizes mm9> mm9.chrom.sizes >>> INFO: trying MySQL /usr/bin/mysql for database mm9 >>> $ sort -k1,1 -k2,2n t.bed | bedItemOverlapCount -chromSize=mm9.chrom.sizes >>> stdin >>> >>> >>> Could you please let know what is the correct way to run >>> bedItemOverlapCount? _______________________________________________ Genome maillist - Genome@lists.soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
