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- /usr/bin/mysql --user=genomep --password=password --host=genome-mysql.cse.ucsc.edu
- -A -D hg38 -e 'select concat(t.name, ".", i.version) name,
- k.locusLinkId as "EntrezId", t.chrom, t.strand, t.txStart,
- t.txEnd, t.cdsStart, t.cdsEnd, t.exonCount, t.exonStarts,
- t.exonEnds, t.score, t.name2 from refGene t join hgFixed.gbCdnaInfo i
- on t.name = i.acc join hgFixed.refLink k on t.name = k.mrnaAcc'
- +-------------+-----------+-------+--------+---------+-------+----------+--------+-----------+--------------------+--------------------+-------+-----------+
- | name | EntrezId | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 |
- +-------------+-----------+-------+--------+---------+-------+----------+--------+-----------+--------------------+--------------------+-------+-----------+
- | NR_046018.2 | 100287102 | chr1 | + | 11873 | 14409 | 14409 | 14409 | 3 | 11873,12612,13220, | 12227,12721,14409, | 0 | DDX11L1 |
- | NR_106918.1 | 102466751 | chr1 | - | 17368 | 17436 | 17436 | 17436 | 1 | 17368, | 17436, | 0 | MIR6859-1 |
- | NR_107062.1 | 102465909 | chr1 | - | 17368 | 17436 | 17436 | 17436 | 1 | 17368, | 17436, | 0 | MIR6859-2 |
- | NR_107063.1 | 102465910 | chr1 | - | 17368 | 17436 | 17436 | 17436 | 1 | 17368, | 17436, | 0 | MIR6859-3 |
- | NR_128720.1 | 103504738 | chr1 | - | 17368 | 17436 | 17436 | 17436 | 1 | 17368, | 17436, | 0 | MIR6859-4 |
- +-------------+-----------+-------+--------+---------+-------+----------+--------+-----------+--------------------+--------------------+-------+-----------+
- $ /usr/bin/mysql --user=genomep --password=password --host=genome-mysql.cse.ucsc.edu -A -D hg38 -e 'select * from knownCanonical limit 5'
- +-------+------------+-----------+-----------+------------+--------------------+
- | chrom | chromStart | chromEnd | clusterId | transcript | protein |
- +-------+------------+-----------+-----------+------------+--------------------+
- | chrX | 100628669 | 100636806 | 1 | uc004ega.3 | ENSG00000000003.14 |
- | chrX | 100584801 | 100599885 | 2 | uc004efy.5 | ENSG00000000005.5 |
- | chr20 | 50934866 | 50958550 | 3 | uc002xvw.2 | ENSG00000000419.12 |
- | chr1 | 169853073 | 169893959 | 4 | uc001ggs.5 | ENSG00000000457.13 |
- | chr1 | 169795048 | 169854080 | 5 | uc001ggp.4 | ENSG00000000460.16 |
- +-------+------------+-----------+-----------+------------+--------------------+
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