Hello, Patrice.
Thank you for your interest in the UCSC Genome Browser and for your question about access to tables.
To better assist you, could you provide more details on what you are trying to do? Both MANE and dgvGold data are offered as bigBeds. We are increasingly moving new data into bigBed format, and we do offer tools such as bigBedToBed, which can be used to obtain only features within a given range without even downloading the entire file
$ bigBedToBed -chrom=chr6 -start=0 -end=1000000 http://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.bb stdout
chr6 292486 351355 ENST00000419235.7 0 + 292539 348951 8,81,156 7 74,34,83,50,75,172,2587, 0,12141,19393,42627,53367,55616,56282, ENST00000419235.7 cmpl cmpl 0,0,1,0,2,2,0, mRNA ENSG00000112679.15 DUSP22 protein_coding ENSP00000397459.2 NM_001286555.3 GeneID:56940 NP_001273484.1 MANE Select
chr6 391751 411443 ENST00000380956.9 0 + 393152 407598 8,81,156 9 58,271,187,89,145,108,354,113,3989, 0,1346,3069,4095,5356,7076,9672,13266,15703, ENST00000380956.9 cmpl cmpl -1,0,0,1,0,1,1,1,0, mRNA ENSG00000137265.16 IRF4 protein_coding ENSP00000370343.4 NM_002460.4 GeneID:3662 NP_002451.2 MANE Select
chr6 485153 693139 ENST00000230449.9 0 - 486670 637818 8,81,156 28 1611,60,62,123,56,142,117,67,62,60,81,62,122,158,66,125,126,119,103,82,146,81,125,114,127,177,161,121, 0,3825,5971,12213,14491,47315,64021,68700,70073,70800,71330,77630,78879,79391,79710,87366,91603,107315,112867,113706,113926,124944,132557,134276,144681,147787,152547,207865, ENST00000230449.9 cmpl cmpl 2,2,0,0,1,0,0,2,0,0,0,1,2,0,0,1,1,2,1,0,1,1,2,2,1,1,0,-1,mRNA ENSG00000112685.14 EXOC2 protein_coding ENSP00000230449.4 NM_018303.6 GeneID:55770 NP_060773.3 MANE Select
chr6 655938 657100 ENST00000380907.3 0 - 656107 656944 8,81,156 1 1162, 0, ENST00000380907.3 cmpl cmpl 0, mRNA ENSG00000188996.5 HUS1B protein_coding ENSP00000370293.2 NM_148959.4 GeneID:135458 NP_683762.2 MANE Select
$ bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvMerged.bb -chrom=chr6 -start=0 -end=100000 stdout
chr6 60000 775274 esv2759401 0 + 60000 60000 139,69,19 gain+loss Redon et al 2006 17122850 BAC aCGH, SNP array esv2757151,esv2758034 270 198 19 NA06985,NA06991,NA06993,NA06994,NA07000,NA07019,NA07034,NA07048,NA07056,NA07345,NA07348,NA10830,NA10831,NA10838,NA10839,NA10846,NA10847,NA10854,NA10855,NA10856,NA10857,NA10859,NA10860,NA10863,NA11829,NA11830,NA11831,NA11832,NA11839,NA11840,NA11993,NA11995,NA12003,NA12004,NA12005,NA12006,NA12044,NA12056,NA12057,NA12144,NA12146,NA12154,NA12156,NA12234,NA12236,NA12239,NA12248,NA12249,NA12264,NA12707,NA12751,NA12752,NA12753,NA12760,NA12761,NA12762,NA12801,NA12802,NA12813,NA12814,NA12815,NA12864,NA12865,NA12873,NA12874,NA12878,NA18500,NA18501,NA18502,NA18503,NA18504,NA18505,NA18508,NA18515,NA18516,NA18517,NA18521,NA18522,NA18523,NA18524,NA18532,NA18537,NA18542,NA18545,NA18547,NA18550,NA18552,NA18558,NA18562,NA18563,NA18566,NA18572,NA18573,NA18582,NA18592,NA18593,NA18594,NA18603,NA18608,NA18609,NA18611,NA18612,NA18620,NA18621,NA18623,NA18624,NA18632,NA18635,NA18637,NA18852,NA18853,NA18854,NA18855,NA18856,NA18857,NA18858,NA18859,NA18860,NA18861,NA18862,NA18863,NA18870,NA18871,NA18872,NA18912,NA18913,NA18914,NA18940,NA18944,NA18945,NA18947,NA18949,NA18951,NA18952,NA18953,NA18956,NA18959,NA18961,NA18965,NA18968,NA18969,NA18972,NA18973,NA18974,NA18975,NA18976,NA18978,NA18980,NA18981,NA18991,NA18994,NA18995,NA18997,NA18998,NA18999,NA19003,NA19005,NA19007,NA19092,NA19093,NA19094,NA19098,NA19099,NA19100,NA19101,NA19102,NA19103,NA19116,NA19119,NA19120,NA19127,NA19128,NA19129,NA19130,NA19131,NA19132,NA19137,NA19138,NA19139,NA19143,NA19144,NA19145,NA19153,NA19154,NA19159,NA19160,NA19161,NA19172,NA19192,NA19193,NA19194,NA19200,NA19201,NA19202,NA19203,NA19204,NA19205,NA19207,NA19208,NA19209,NA19210,NA19211,NA19221,NA19222,NA19223,NA19238,NA19239,NA19240 715274
chr6 60000 653718 nsv428134 0 + 60000 60000 0,0,200 gain Perry et al 2008b 18775914 BAC aCGH, FISH, PCR nssv450589,nssv450603,nssv450588,nssv450586,nssv450578,nssv450596,nssv450597,nssv450599,nssv450602,nssv450585,nssv450600,nssv450582,nssv450594,nssv450579,nssv450595,nssv450601,nssv450584,nssv450591,nssv450593,nssv450580,nssv450590,nssv450581,nssv450583,nssv450592 62 24 0 HGDP00449,HGDP00450,HGDP00460,HGDP00463,HGDP00467,HGDP00471,HGDP00474,HGDP00476,HGDP00984,HGDP00986,HGDP01087,HGDP01088,HGDP01089,HGDP01093,HGDP01094,NA18498,NA18916,NA19096,NA19108,NA19113,NA19147,NA19181,NA19189,NA19257 593718
chr6 60000 126418 nsv10796 0 + 60000 60000 139,69,19 gain+loss Perry et al 2008 18304495 Oligo aCGH nssv16470,nssv13892,nssv14496,nssv13150,nssv12829,nssv14374,nssv15673,nssv14158,nssv15703,nssv15831,nssv15807,nssv13965,nssv13884,nssv15001,nssv13880,nssv15861 31 11 3 NA07029,NA10839,NA10863,NA12802,NA18504,NA18537,NA18572,NA18853,NA18860,NA18975,NA19132,NA19144,NA19221,NA19240 66418
chr6 60000 85500 nsv1151792 0 + 60000 60000 0,0,200 duplication John et al 2014 26484159 Sequencing nssv3998974 1 1 0 KWB1 25500
chr6 60000 79325 nsv4121945 0 + 60000 60000 0,0,200 duplication gnomAD Structural Variants 32461652 Sequencing nssv15977875 10847 1 0 19325
chr6 60030 155228 nsv820764 0 + 60030 60030 200,0,0 deletion Ju et al 2010 20802225 Sequencing nssv1420566 1 0 1 NA10851 95198
chr6 60030 149517 esv26003 0 + 60030 60030 0,0,200 gain Conrad et al 2009 19812545 Oligo aCGH esv20531,esv19428,esv13218 40 31 0 NA06985,NA07037,NA11894,NA11993,NA11995,NA12006,NA12156,NA12239,NA12287,NA12749,NA12776,NA12828,NA12878,NA15510,NA18502,NA18505,NA18508,NA18511,NA18523,NA18858,NA18861,NA18907,NA18909,NA18916,NA19099,NA19114,NA19129,NA19147,NA19190,NA19225,NA19240 89487
chr6 60198 63400 nsv1076592 0 + 60198 60198 0,0,200 duplication Thareja et al 2015 25765185 Sequencing nssv3770858 1 1 0 KWP1 3202
chr6 61999 102888 nsv969341 0 + 61999 61999 0,0,200 duplication Sudmant et al 2013 23825009 Oligo aCGH, Sequencing nssv2390986,nssv2390943,nssv2390983,nssv2391001,nssv2390989,nssv2390951,nssv2390984,nssv2390948,nssv2390981,nssv2390997,nssv2390974,nssv2390959,nssv2390979,nssv2390144,nssv2390969,nssv2390945,nssv2390972,nssv2390999,nssv2390991,nssv2390956,nssv2390992,nssv2390966,nssv2390976,nssv2390950,nssv2390978,nssv2390949,nssv2390990,nssv2390958,nssv2390973,nssv2390960,nssv2390994,nssv2390961,nssv2390970,nssv2390944,nssv2390977,nssv2390133,nssv2390993,nssv2390142,nssv2390985,nssv2390954,nssv2390982,nssv2390141,nssv2390968,nssv2390139,nssv2390988,nssv2390138,nssv2390987,nssv2390995,nssv2390971,nssv2390965,nssv2390980,nssv2390942,nssv2390975,nssv2390140,nssv2390143,nssv2391003,nssv2390955,nssv2390946,nssv2390998,nssv2390136,nssv2390963,nssv2390962,nssv2391004,nssv2390953,nssv2390964,nssv2390940,nssv2390996,nssv2390147,nssv2390134,nssv2391000,nssv2390941,nssv2390146,nssv2390137,nssv2390947,nssv2390967,nssv2390957,nssv2390145,nssv2390952,nssv2390135,nssv2391002 97 10 0 HGDP00456,HGDP00521,HGDP00542,HGDP00665,HGDP00778,HGDP00927,HGDP00998,HGDP01029,HGDP01284,HGDP01307 40889
chr6 62051 63550 dgv3436e59 0 + 62051 62051 0,0,200 duplication 1000 Genomes Consortium Pilot Project 20981092 Digital array, Oligo aCGH, PCR, Sequencing esv3398664,esv3427645,esv3363772 185 3 0 NA19238,NA19239,NA19240 1499
chr6 62099 69700 nsv1139856 0 + 62099 62099 0,0,200 duplication Alsmadi et al 2014 24896259 Sequencing nssv3978192 2 1 0 KWS2 7601
chr6 66999 111000 nsv4125160 0 + 66999 66999 200,0,0 deletion gnomAD Structural Variants 32461652 Sequencing nssv15907097 10847 0 1 44001
chr6 67300 82100 nsv3386669 0 + 67300 67300 0,0,200 duplication Audano et al 2019 30661756 Sequencing nssv14729633,nssv14724650,nssv14723515 14 3 0 HG00733,NA12878,NA19240 14800
chr6 68051 70850 esv3348565 0 + 68051 68051 0,0,200 duplication 1000 Genomes Consortium Pilot Project 20981092 Digital array, Oligo aCGH, PCR, Sequencing essv8695032 185 1 0 NA19240 2799
chr6 69199 72000 nsv1128922 0 + 69199 69199 0,0,200 duplication Alsmadi et al 2014 24896259 Sequencing nssv3961592 2 1 0 KWS1 2801
chr6 70844 202392 dgv1068e199 0 + 70844 70844 200,0,0 deletion 1000 Genomes Consortium Phase 1 23128226 Merging, Oligo aCGH, PCR, Sequencing, SNP array esv2671556,esv2678528,esv2663786 1151 0 226 HG01515,HG01516,HG01518,HG01519,HG01521,HG01522,NA18526,NA18530,NA18532,NA18534,NA18535,NA18536,NA18537,NA18538,NA18539,NA18541,NA18542,NA18543,NA18544,NA18545,NA18546,NA18547,NA18548,NA18549,NA18552,NA18553,NA18555,NA18557,NA18558,NA18559,NA18560,NA18561,NA18562,NA18563,NA18564,NA18565,NA18566,NA18567,NA18570,NA18571,NA18572,NA18573,NA18574,NA18576,NA18577,NA18579,NA18582,NA18592,NA18593,NA18595,NA18597,NA18599,NA18602,NA18603,NA18605,NA18606,NA18608,NA18609,NA18610,NA18611,NA18612,NA18613,NA18614,NA18615,NA18616,NA18617,NA18618,NA18620,NA18621,NA18622,NA18623,NA18624,NA18626,NA18627,NA18628,NA18630,NA18631,NA18632,NA18633,NA18634,NA18635,NA18636,NA18637,NA18638,NA18940,NA18941,NA18942,NA18943,NA18944,NA18945,NA18947,NA18948,NA18949,NA18950,NA18951,NA18952,NA18953,NA18956,NA18959,NA18960,NA18961,NA18963,NA18964,NA18965,NA18971,NA18973,NA18980,NA18982,NA18983,NA18984,NA18985,NA18986,NA18987,NA18988,NA18989,NA18990,NA18999,NA19000,NA19003,NA19004,NA19005,NA19007,NA19009,NA19010,NA19012,NA19055,NA19056,NA19057,NA19058,NA19059,NA19060,NA19062,NA19063,NA19064,NA19065,NA19066,NA19067,NA19068,NA19070,NA19072,NA19074,NA19075,NA19076,NA19077,NA19078,NA19079,NA19080,NA19081,NA19083,NA19084,NA19087,NA19088,NA20503,NA20504,NA20505,NA20506,NA20507,NA20508,NA20509,NA20510,NA20512,NA20515,NA20516,NA20517,NA20518,NA20519,NA20520,NA20522,NA20524,NA20525,NA20527,NA20528,NA20529,NA20531,NA20532,NA20534,NA20535,NA20538,NA20539,NA20541,NA20542,NA20543,NA20544,NA20582,NA20585,NA20586,NA20588,NA20589,NA20752,NA20753,NA20754,NA20756,NA20757,NA20758,NA20759,NA20760,NA20761,NA20765,NA20766,NA20768,NA20769,NA20770,NA20771,NA20773,NA20778,NA20783,NA20785,NA20790,NA20792,NA20795,NA20796,NA20798,NA20799,NA20800,NA20801,NA20802,NA20804,NA20807,NA20810,NA20811,NA20814,NA20815,NA20816,NA20818,NA20819,NA20828 131548
chr6 75558 76650 nsv3383057 0 + 75558 75558 0,0,0 line1 deletion Audano et al 2019 30661756 Sequencing nssv14776456 14 0 1 HG02059 1092
chr6 76851 77650 esv3328489 0 + 76851 76851 0,0,200 duplication 1000 Genomes Consortium Pilot Project 20981092 Digital array, Oligo aCGH, PCR, Sequencing essv8695193 185 1 0 NA19239 799
chr6 86298 118800 nsv1073944 0 + 86298 86298 200,0,0 deletion Thareja et al 2015 25765185 Sequencing nssv3763139 1 0 1 KWP1 32502
chr6 86699 98400 nsv4117238 0 + 86699 86699 200,0,0 deletion gnomAD Structural Variants 32461652 Sequencing nssv15907098 10847 0 1 11701
chr6 88549 88626 nsv3379713 0 + 88549 88549 0,0,0 line1 deletion Audano et al 2019 30661756 Sequencing nssv14786231 14 0 1 HG02059 77
chr6 88646 88721 nsv3383240 0 + 88646 88646 200,0,0 deletion Audano et al 2019 30661756 Sequencing nssv14714856 14 0 1 HG02059 75
chr6 88851 90150 dgv3437e59 0 + 88851 88851 0,0,200 duplication 1000 Genomes Consortium Pilot Project 20981092 Digital array, Oligo aCGH, PCR, Sequencing esv3388723,esv3386561 185 2 0 NA19239,NA19240 1299
chr6 89140 89678 nsv3389545 0 + 89140 89140 200,0,0 deletion Audano et al 2019 30661756 Sequencing nssv14717010 14 0 1 HG02059 538
chr6 89515 89593 nsv3383561 0 + 89515 89515 200,0,0 deletion Audano et al 2019 30661756 Sequencing nssv14723320 14 0 1 NA12878 78
chr6 89969 90124 nsv3394774 0 + 89969 89969 200,0,0 deletion Audano et al 2019 30661756 Sequencing nssv14713042 14 0 1 HG02059 155
chr6 91799 93900 nsv1119065 0 + 91799 91799 200,0,0 deletion Alsmadi et al 2014 24896259 Sequencing nssv3981864 2 0 1 KWS1 2101
chr6 95399 96100 nsv1126738 0 + 95399 95399 200,0,0 deletion Alsmadi et al 2014 24896259 Sequencing nssv3985006 2 0 1 KWS1 701
chr6 98699 110100 nsv1145084 0 + 98699 98699 200,0,0 deletion Alsmadi et al 2014 24896259 Sequencing nssv3981704 2 0 1 KWS1 11401
You can download the bigBedToBed utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find bigBedToBed under the directory that matches your operating system. For example, here is the direct link for Linux: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed
You can also access the data from these tracks using the Table Browser, and the API:
https://api.genome.ucsc.edu/getData/track?genome=hg38;track=mane;chrom=chr6;start=0;end=1000000
https://api.genome.ucsc.edu/getData/track?genome=hg38;track=dgvGold;chrom=chr6;start=0;end=100000
I hope this is helpful. Please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
