On a related note, featureBits also accepts chromSizes but, as far as I could see from the code, still sets up a mysql connection, even when the chromSizes file is specified.
cheers Max On Tue, Apr 6, 2010 at 4:46 AM, Hiram Clawson <[email protected]> wrote: > 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 - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
