Wednesday, June 10, 2015

UCSC mysql server for interactive queries

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select name,chrom,chromStart,chromEnd,observed from snp130 where name="rs35568883"'
 Results will look like:
 +------------+-------+------------+----------+----------+
| name       | chrom | chromStart | chromEnd | observed |
+------------+-------+------------+----------+----------+
| rs35568883 | chr21 |   38782125 | 38782126 | A/G      |
+------------+-------+------------+----------+----------+
 Now you may want to use hg19 and dbSNP142 for updated results. 

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