Hello Peng, Do you have a local database loaded? If you do, then you should have a .hg.conf file in your home directory (which is why the first command string did not work - it could not locate your .hg.conf file.).
If you do not have a local database, then fetchChromSizes would not work either, as it also requires a database connection. Or did you use the public mySQL server to obtain the data? Or another method? Does your mm9.chrom.sizes file contain data? If not, create one, then re-run the program. Public mySQL server help: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 Thanks, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ 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
