Hi, I'm loking at the data I downloaded from you, and I'm not quite sure that I understand the meaning of the columns.
the data I downloaded are these: rsync -avz --progress rsync://hgdownload.cse.ucsc.edu/goldenPath/ce4/database/nucleosomeFragmentsSense.txt.gz which come from Valouev et al. Genome Res. 18(7), 1051-1063 (2008) I used describe table to figure out what the columns mean, they tell you this: mysql> describe nucleosomeFragmentsSense; +-------------+----------------------+------+-----+---------+-------+ | Field | Type | Null | Key | Default | Extra | +-------------+----------------------+------+-----+---------+-------+ | bin | smallint(5) unsigned | NO | | 0 | | | chrom | varchar(255) | NO | MUL | | | | chromStart | int(10) unsigned | NO | | 0 | | | chromEnd | int(10) unsigned | NO | | 0 | | | name | varchar(255) | NO | | | | | score | int(10) unsigned | NO | | 0 | | | strand | char(1) | NO | | | | | thickStart | int(10) unsigned | NO | | 0 | | | thickEnd | int(10) unsigned | NO | | 0 | | | reserved | int(10) unsigned | NO | | 0 | | | blockCount | int(10) unsigned | NO | | 0 | | | blockSizes | longblob | NO | | | | | chromStarts | longblob | NO | | | | +-------------+----------------------+------+-----+---------+-------+ I've interpreted the 'score' column as the number of reads at the given position. is this correct? Thanks very much for your help, George Locke > > Good point! I forgot to add db in my example too. > > -Galt > > > On Fri, 28 Aug 2009, Michael Pheasant wrote: > >> Try specifying the database you want for example: > > mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A hg18 > > Dont know what database you want though; hg19, mm9, etc > > M > > On Fri, Aug 28, 2009 at 7:19 AM, GEORGE LOCKE<[email protected]> > wrote: >> Hi, >> >> I'm a grad student at Rutgers trying to get access to data from the >> genome >> browser mysql database.  I'm doing research in nucleosome positioning >> with >> Prof. Alex Morozov. >> >> i logged on as suggested, mysql --user=genome >> --host=genome-mysql.cse.ucsc.edu -A >> >> this is the query I wish to execute: >> select chrom, chromStart, chromEnd, score, strand from >> nucleosomeFragmentsSense into outfile "dump.txt"; >> (using database ce4) >> >> this is the error i get: ERROR 1045 (28000): Access denied for user >> 'genome'@'%' (using password: NO) >> >> what can I do?  I can't find this information in text format anywhere >> and >> hoped I could just get it direct from the database but have been >> rebuffed. >> >> Regards, >> George >> >> _______________________________________________ >> Genome maillist  -  [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > > > -- > Michael Pheasant > Associate Project Scientist > UCSC Genome Browser > > Email: [email protected] > Skype: mpheasant > Phone: +1-831-459-1424 > > Location: Engineering2 Room 515 > Post: CBSE, UC Santa Cruz, MS:CBSE/ITI > 1156 High Street > Santa Cruz, CA 95064, USA > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
