Try this George: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/ce4/database/nucleosomeFragmentsSense.txt.gz .
That is the entire database table already dumped in text format. Also available via: wget --timestamping \ ftp://hgdownload.cse.ucsc.edu/goldenPath/ce4/database/nucleosomeFragmentsSense.txt.gz Your mysql query can fetch the data: mysql --user=genome -host=genome-mysql.cse.ucsc.edu -A \ -e "your select statement;" ce4 | gzip -c > nucleosomeFragmentsSense.txt.gz But I suspect the rsync command above will be the most efficient mechanism of transfer. To get the columns you want out of that file: zcat nucleosomeFragmentsSense.txt.gz | awk -F'\t' '{print $2,$3,$4,$6,$7}' --Hiram GEORGE LOCKE 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
