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
