Hello Peng, There is a correction and some more information:
Your usage for bedItemOverlapCount when using a chrom.sizes file is correct. This means that the one of the inputs has a problem. The program fetchChromSizes does not require a local database, I was wrong in my earlier email. However, it does need to reach UCSC through one of the methods it uses to retrieve data (one of which is mySQL). If you want, you could simply ftp download the file for mm9 from here (maybe to confirm your copy?): http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ If chrom.sizes is OK, the next issue to address is the BED input data. The sort method is likely the source of the problem. The order of the chromosomes must match the order in chrom.sizes exactly. The default unix sort order (as you use it with column 1 in the input file) will not achieve this ordering. For your other related question, it was suggested here that instead of wgEncode, it would be better to use wigToBigWig. We are updating the bedItemOverlapCount program documentation to include a usage statement for using bigWig files. The program wgEncode is being retired. Once the usage for bedItemOverlapCount is posted, a precompiled version of wigToBigWig can be downloaded here: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ We will send you an email once the program bedItemOverlapCount is updated and published. Thank you for your patience. All feedback is welcomed. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/5/10 5:48 PM, Jennifer Jackson wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
