How to retrieve the chromosomal coordinates for a list of DNA markers ?
1 answer
using ucsc+mysql
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select S.chrom,S.chromStart,S.chromEnd,A.alias from stsMap as S, stsAlias as A where A.alias in ("D1S216","D1S2829","D3S1265") and A.identNo=S.identNo'
+-------+------------+-----------+---------+
| chrom | chromStart | chromEnd | alias |
+-------+------------+-----------+---------+
| chr1 | 68252504 | 68252812 | D1S2829 |
| chr1 | 77655323 | 77655608 | D1S216 |
| chr3 | 195526029 | 195526304 | D3S1265 |
+-------+------------+-----------+---------+
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Ram
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Pierre Lindenbaum
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written
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Pierre Lindenbaum
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