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Buttonwood/refGene.sql

Created March 13, 2015 07:27
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gff to store in mysql
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refGene.sql
CREATE TABLE `refGene` (
`bin` smallint(5) unsigned NOT NULL,
`name` varchar(255) NOT NULL,
`chrom` varchar(255) NOT NULL,
`strand` char(1) NOT NULL,
`txStart` int(10) unsigned NOT NULL,
`txEnd` int(10) unsigned NOT NULL,
`cdsStart` int(10) unsigned NOT NULL,
`cdsEnd` int(10) unsigned NOT NULL,
`exonCount` int(10) unsigned NOT NULL,
`exonStarts` longblob NOT NULL,
`exonEnds` longblob NOT NULL,
`score` int(11) DEFAULT NULL,
`name2` varchar(255) NOT NULL,
`cdsStartStat` enum('none','unk','incmpl','cmpl') NOT NULL,
`cdsEndStat` enum('none','unk','incmpl','cmpl') NOT NULL,
`exonFrames` longblob NOT NULL,
KEY `chrom` (`chrom`,`bin`),
KEY `name` (`name`),
KEY `name2` (`name2`)
)
@Buttonwood

Buttonwood commented Mar 13, 2015

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2 NM_178565.4 chr8 - 108911543 109095913 108913302 109094866 6 108911543,108970307,108972901,109001283,109094772,109095424, 108913418,108970496,108973045,109001472,109095035,109095913, 0 RSPO2 cmpl cmpl 1,1,1,1,0,-1,
917 NM_020630.4 chr10 + 43572516 43622952 43572706 43622202 19 43572516,43595906,43597789,43600399,43601823,43604478,43606654,43607546,43608300,43609003,43609927,43612031,43613820,43614978,43615528,43617393,43619118,43620330,43622022, 43572779,43596170,43598077,43600641,43602019,43604678,43606913,43607672,43608411,43609123,43610184,43612179,43613928,43615193,43615651,43617464,43619256,43620430,43622952, 0RET cmpl cmpl 0,1,1,1,0,1,0,1,1,1,1,0,1,1,0,0,2,2,0,
2 NM_001282863.1 chr8 - 108911543 109095431 108913302 109094866 5 108911543,108970307,108972901,109094772,109095151, 108913418,108970493,108973045,109095035,109095431, 0 RSPO2 cmpl cmpl 1,1,1,0,-1,

113 NM_001135099.1 chr21 - 42836477 42838080
113 NM_001135099.1 chr21 - 42839660 42839813
113 NM_001135099.1 chr21 - 42840322 42840465
113 NM_001135099.1 chr21 - 42842574 42842670
113 NM_001135099.1 chr21 - 42843732 42843908
113 NM_001135099.1 chr21 - 42845251 42845423
113 NM_001135099.1 chr21 - 42848503 42848547
113 NM_001135099.1 chr21 - 42851098 42851209
113 NM_001135099.1 chr21 - 42852402 42852529
113 NM_001135099.1 chr21 - 42860320 42860440
113 NM_001135099.1 chr21 - 42861433 42861520

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