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mysql获取ucsc信息

已有 3847 次阅读 2013-8-27 12:37 |个人分类:基因组工具|系统分类:科研笔记| Mysql, ucsc

cisgenome注释peaksshi时要用到ucscde的refgene table,我总是会忘记它的title,得到结果时没法跟人交代每一列是什么意思。赶紧记一下一种简单的方法:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select * from refGene where name="NM_000038"'

会返回:

| bin  | name      | chrom | strand | txStart   | txEnd     | cdsStart  | cdsEnd    | exonCount | exonStarts | exonEnds  | score | name2 | cdsStartStat | cdsEndStat | exonFrames  |

+------+-----------+-------+--------+-----------+-----------+-----------+-----------+-----------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------+-------+-------+--------------+------------+-----------------------------------+

| 1440 | NM_000038 | chr5  | +      | 112073555 | 112181936 | 112090587 | 112179823 |        16 | 112073555,112090569,112102022,112102885,112111325,112116486,112128142,112136975,112151191,112154662,112157592,112162804,112163625,112164552,112170647,112173249, | 112073622,112090722,112102107,112103087,112111434,112116600,112128226,112137080,112151290,112155041,112157688,112162944,112163703,112164669,112170862,112181936, |     0 | APC   | cmpl         | cmpl       | -1,0,0,1,2,0,0,0,0,0,1,1,0,0,0,2, |

mysql直接读ucsc数据库会给人很多惊喜的。



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