Hi all,
I want to extract the coordinates of each genes in hg19 from their -2000bp of TSS to the end of first exon. So I downloaded the bed file from UCSC. The files are like this:
can someone tell me the meaning of each column? I found a description of bed files in the UCSC table browser, but it doesn't seem to match the file I downloaded.
thanks
I want to extract the coordinates of each genes in hg19 from their -2000bp of TSS to the end of first exon. So I downloaded the bed file from UCSC. The files are like this:
Code:
track name="tb_refGene" description="table browser query on refGene" visibility=3 url= chr1 66999824 67210768 NM_032291 0 + 67000041 67208778 0 25 227,64,25,72,57,55,176,12,12,25,52,86,93,75,501,128,127,60,112,156,133,203,65,165,2013, 0,91705,98928,101802,105635,108668,109402,126371,133388,136853,137802,139139,142862,145536,147727,155006,156048,161292,185152,195122,199606,205193,206516,207130,208931, chr1 33546713 33586132 NM_052998 0 + 33547850 33585783 0 12 182,121,212,177,174,173,135,166,163,113,215,488, 0,275,488,1065,2841,10937,12169,13435,15594,16954,36789,38931, chr1 33546713 33586132 NM_001293562 0 + 33547850 33585783 0 11 182,118,177,174,173,135,166,163,113,215,488, 0,278,1065,2841,10937,12169,13435,15594,16954,36789,38931, chr1 25071759 25170815 NM_013943 0 + 25072044 25167428 0 6 357,110,126,107,182,3552, 0,52473,68825,81741,94591,95504, chr1 48998526 50489626 NM_032785 0 - 48999844 50489468 0 14 1439,27,97,163,153,112,115,90,40,217,95,125,123,192, 0,2035,6787,54149,57978,101638,120482,130297,334336,512729,712915,1164458,1318541,1490908, chr1 16767166 16786584 NM_001145277 0 + 16767256 16785491 0 7 182,101,105,82,109,178,1248, 0,2960,7198,7388,8421,11166,18170, chr1 16767166 16786584 NM_001145278 0 + 16767256 16785385 0 8 104,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170, chr1 16767166 16786584 NM_018090 0 + 16767256 16785385 0 8 182,101,105,82,109,178,76,1248, 0,2960,7198,7388,8421,11166,15146,18170, chr1 8378144 8404227 NM_001080397 0 + 8378168 8404073 0 9 102,421,93,225,728,154,177,206,421, 0,6221,7213,7733,12124,17352,19731,21408,25662, chr1 92145899 92351836 NM_001195683 0 - 92149295 92327088 0 17 3515,108,42,121,300,159,141,153,335,190,148,169,184,138,185,174,402, 0,15329,17746,28320,31900,35893,36225,38969,39550,41612,47316,49462,54433,78270,116944,181128,205535, chr1 92145899 92351836 NR_036634 0 - 92351836 92351836 0 18 3515,108,42,121,300,159,141,153,338,190,148,169,184,138,185,97,174,402, 0,15329,17746,28320,31900,35893,36225,38969,39550,41612,47316,49462,54433,78270,116944,120616,181128,205535, chr1 92145899 92351836 NM_003243 0 - 92149295 92327088 0 17 3515,108,42,121,300,159,141,153,338,190,148,169,184,138,185,174,402, 0,15329,17746,28320,31900,35893,36225,38969,39550,41612,47316,49462,54433,78270,116944,181128,205535, chr1 92145899 92371559 NM_001195684 0 - 92149295 92327088 0 18 3515,108,42,121,300,159,141,153,335,190,148,169,184,138,185,174,61,177, 0,15329,17746,28320,31900,35893,36225,38969,39550,41612,47316,49462,54433,78270,116944,181128,219294,225483, chr1 100652477 100715409 NM_001918 0 - 100661810 100715376 0 11 9501,72,192,78,167,217,122,182,76,124,84, 0,19308,19523,23772,27895,29061,31704,43811,48514,53839,62848, chr1 175913961 176176380 NM_022457 0 - 175914288 176176114 0 20 345,45,161,125,118,117,82,109,144,136,115,58,77,60,69,120,77,98,60,673, 0,2369,42117,43462,44536,82746,98360,98884,101355,136326,140950,171798,190184,191662,204180,218043,218989,231084,239807,261746, chr1 184356149 184598155 NM_030806 0 + 184446643 184588690 0 6 353,218,95,77,61,9504, 0,90370,120572,203723,211385,232502, chr1 150980972 151008189 NM_021222 0 + 150981108 151006710 0 8 175,93,203,185,159,95,159,1908, 0,9315,9970,16114,17018,18736,20289,25309,
Code:
bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames 138 NM_016166 chr15 + 68346571 68480404 68346664 68480173 14 68346571,68378643,68434283,68434627,68438153,68438903,68445927,68457068,68466069,68467974,68468811,68473549,68475967,68479879, 68346688,68379088,68434368,68434675,68438244,68439038,68446033,68457142,68466230,68468105,68468992,68473692,68476005,68480404, 0 PIAS1 cmpl cmpl 0,0,1,2,2,0,0,1,0,2,1,2,1,0, 636 NM_016162 chr12 - 6759703 6772308 6760360 6772267 8 6759703,6760489,6761436,6761827,6762101,6762395,6765892,6772230, 6760400,6760551,6761584,6761933,6762216,6762562,6765964,6772308, 0 ING4 cmpl cmpl 2,0,2,1,0,1,1,0, 1314 NM_016156 chr11 - 95566043 95657371 95568453 95657118 15 95566043,95569311,95571257,95574780,95578116,95580877,95582837,95583763,95590715,95591694,95595155,95595435,95598764,95621319,95 ... 95568615,95569488,95571371,95574873,95578323,95581063,95583026,95583913,95590799,95591796,95595266,95595530,95598840,95621425,95 ... 0 MTMR2 cmpl cmpl 0,0,0,0,0,0,0,0,0,0,0,1,0,2,0, 858 NM_006739 chr22 + 35796115 35820495 35796431 35820248 17 35796115,35796423,35799199,35799406,35802545,35804400,35806736,35808502,35809867,35811821,35812331,35812630,35813736,35815876,35 ... 35796201,35796598,35799326,35799535,35802718,35804556,35806903,35808674,35809979,35811965,35812397,35812807,35813849,35816005,35 ... 0 MCM5 cmpl cmpl -1,0,2,0,0,2,2,1,2,0,0,0,0,2,2,1,0, 1761 NM_032385 chr5 - 154198051 154230213 154199875 154217738 9 154198051,154200819,154202031,154202946,154210360,154214184,154214402,154217690,154230042, 154200032,154200986,154202137,154203152,154210482,154214288,154214494,154217738,154230213, 0 FAXDC2 cmpl cmpl 2,0,2,0,1,2,0,0,-1, 587 NM_021034 chr11 - 319672 320914 319837 320813 2 319672,320564, 319990,320914, 0 IFITM3 cmpl cmpl 0,0, 1162 NM_020932 chrX + 75648045 75651746 75648323 75651197 1 75648045, 75651746, 0 MAGEE1 cmpl cmpl 0, 13 NM_020929 chr11 - 40135750 41481186 40135919 40137842 5 40135750,40162350,40341177,40669691,41480980, 40137884,40162403,40341271,40669828,41481186, 0 LRRC4C cmpl cmpl 0,-1,-1,-1,-1, 1352 NM_021029 chrX + 100645877 100651142 100645923 100650736 5 100645877,100646446,100646742,100650322,100650715, 100646034,100646552,100646810,100650445,100651142, 0 RPL36A cmpl cmpl 0,0,1,0,0, 1688 NM_032378 chr8 - 144661866 144679845 144661961 144672251 10 144661866,144662181,144662675,144663223,144663398,144668388,144668898,144671160,144672777,144679517, 144662000,144662376,144662897,144663324,144663498,144668460,144669022,144672251,144672908,144679845, 0 EEF1D cmpl cmpl 0,0,0,1,0,0,2,0,-1,-1,
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