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Forked from slowkow/hg19.rRNA.interval_list
Last active March 14, 2018 09:36
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@HD VN:1.4 SO:coordinate
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
chr1 9497728 9497837 - ENST00000517147.1
chr1 13949679 13949779 - ENST00000411020.1
chr1 34578550 34578664 + ENST00000364278.1
chr1 37730278 37730387 - ENST00000516559.1
chr1 39619836 39619968 - ENST00000410446.1
chr1 41932608 41932699 - ENST00000516754.1
chr1 43662088 43662207 + ENST00000362370.1
chr1 45397995 45398103 + ENST00000517230.1
chr1 52439082 52439207 + ENST00000363969.1
chr1 63652007 63652121 - ENST00000516450.1
chr1 74215200 74215306 - ENST00000363731.1
chr1 78080554 78080637 + ENST00000515976.1
chr1 78245589 78245684 + ENST00000410917.1
chr1 78560491 78560599 - ENST00000365393.1
chr1 78840849 78840953 - ENST00000391006.1
chr1 86349363 86349481 - ENST00000364750.1
chr1 87918923 87919056 - ENST00000362448.1
chr1 93953890 93954009 - ENST00000391299.1
chr1 111584456 111584547 + ENST00000516951.1
chr1 117504969 117505093 - ENST00000516701.1
chr1 118806995 118807112 - ENST00000410277.1
chr1 146124161 146124283 + ENST00000459463.1
chr1 147665993 147666115 + ENST00000459025.1
chr1 148913273 148913382 - ENST00000410922.1
chr1 159148263 159148349 + ENST00000410620.1
chr1 162308433 162308532 + ENST00000516453.1
chr1 163438286 163438395 - ENST00000363457.1
chr1 163479274 163479385 + ENST00000391225.1
chr1 166011481 166011587 + ENST00000384611.1
chr1 166975196 166975314 + ENST00000363166.1
chr1 169036502 169036602 + ENST00000517178.1
chr1 173890208 173890338 + ENST00000516422.1
chr1 173938456 173938574 - ENST00000363885.1
chr1 178530048 178530164 + ENST00000364477.1
chr1 181740702 181740780 + ENST00000517168.1
chr1 182913500 182913625 - ENST00000362967.1
chr1 184984083 184984199 - ENST00000364442.1
chr1 189635279 189635386 - ENST00000516744.1
chr1 204531541 204531649 - ENST00000363538.1
chr1 204676448 204676558 - ENST00000516841.1
chr1 219935131 219935217 + ENST00000516277.1
chr1 227748882 227749001 + ENST00000365394.1
chr1 228743494 228743602 + ENST00000365186.1
chr1 228746015 228746133 - ENST00000362482.1
chr1 228748256 228748374 - ENST00000364718.1
chr1 228750497 228750615 - ENST00000362467.1
chr1 228752738 228752856 - ENST00000363511.1
chr1 228754979 228755097 - ENST00000362526.1
chr1 228757194 228757312 - ENST00000363754.1
chr1 228759414 228759532 - ENST00000365651.1
chr1 228761656 228761774 - ENST00000363473.1
chr1 228763895 228764013 - ENST00000364451.1
chr1 228766137 228766255 - ENST00000363040.1
chr1 228768378 228768496 - ENST00000362464.1
chr1 228770618 228770736 - ENST00000362400.1
chr1 228772843 228772961 - ENST00000365656.1
chr1 228775084 228775202 - ENST00000364485.1
chr1 228777315 228777433 - ENST00000365055.1
chr1 228779556 228779674 - ENST00000365387.1
chr1 228781787 228781905 - ENST00000363500.1
chr1 228783659 228783779 - ENST00000390935.1
chr1 229685652 229685769 + ENST00000364622.1
chr1 230955996 230956104 + ENST00000365193.1
chr1 231417160 231417270 - ENST00000410475.1
chr1 242297574 242297683 + ENST00000410188.1
chr1 247367872 247367963 - ENST00000516707.1
chr2 11657523 11657629 + ENST00000364740.1
chr2 11701787 11701905 - ENST00000365378.1
chr2 20601388 20601485 - ENST00000390869.1
chr2 22561758 22561875 - ENST00000384155.1
chr2 24787499 24787607 - ENST00000365560.1
chr2 28906842 28906949 + ENST00000410300.1
chr2 31451178 31451276 + ENST00000364801.1
chr2 33510836 33510954 - ENST00000390902.1
chr2 33557965 33558074 + ENST00000516437.1
chr2 56462352 56462465 - ENST00000362525.1
chr2 59921897 59922004 + ENST00000516917.1
chr2 61225887 61226023 + ENST00000410319.1
chr2 69409029 69409135 - ENST00000516041.1
chr2 74195250 74195333 - ENST00000365006.1
chr2 77000035 77000171 + ENST00000363158.1
chr2 81723338 81723451 - ENST00000364020.1
chr2 91862883 91862992 + ENST00000410903.1
chr2 97622445 97622552 - ENST00000517036.1
chr2 125690492 125690597 + ENST00000516865.1
chr2 129202655 129202772 - ENST00000459503.1
chr2 133010727 133010878 - ENST00000365304.1
chr2 134988766 134988883 + ENST00000410989.1
chr2 138269668 138269780 - ENST00000391123.1
chr2 148471024 148471123 - ENST00000517274.1
chr2 155446919 155447040 + ENST00000411358.1
chr2 162266065 162266181 + ENST00000605921.1
chr2 163353446 163353561 + ENST00000391010.1
chr2 165714942 165715056 + ENST00000362638.1
chr2 165752187 165752287 - ENST00000411386.1
chr2 178003427 178003525 + ENST00000515937.1
chr2 182913549 182913632 + ENST00000410486.1
chr2 189141459 189141571 - ENST00000363780.1
chr2 201713761 201713867 - ENST00000411160.1
chr2 208918885 208918982 - ENST00000516132.1
chr2 209785271 209785388 - ENST00000365294.1
chr2 210586637 210586745 - ENST00000410385.1
chr2 212400378 212400494 + ENST00000362715.1
chr2 217658212 217658323 - ENST00000410900.1
chr2 228627768 228627868 - ENST00000516537.1
chr2 242524383 242524490 + ENST00000384457.1
chr3 12552594 12552712 - ENST00000363244.1
chr3 14436148 14436257 + ENST00000362739.1
chr3 25066498 25066617 + ENST00000364843.1
chr3 25393775 25393883 - ENST00000365092.1
chr3 31270207 31270339 + ENST00000411051.1
chr3 33533475 33533590 - ENST00000365305.1
chr3 37383140 37383257 + ENST00000410276.1
chr3 49504548 49504661 - ENST00000364431.1
chr3 50457212 50457330 + ENST00000365452.1
chr3 51728481 51728598 - ENST00000364725.1
chr3 56219132 56219250 + ENST00000363368.1
chr3 63531116 63531211 + ENST00000516492.1
chr3 68932118 68932242 + ENST00000517019.1
chr3 72740856 72740962 - ENST00000410906.1
chr3 124777148 124777282 - ENST00000516833.1
chr3 126283408 126283521 - ENST00000365098.1
chr3 127682451 127682567 + ENST00000364340.1
chr3 133428920 133429011 - ENST00000364524.1
chr3 134502278 134502397 - ENST00000364543.1
chr3 137236976 137237097 - ENST00000364455.1
chr3 142310519 142310633 - ENST00000516936.1
chr3 143905747 143905862 - ENST00000410846.1
chr3 150905886 150906010 + ENST00000363124.1
chr3 156891707 156891829 - ENST00000410743.1
chr3 176481021 176481129 + ENST00000516493.1
chr3 178146985 178147078 - ENST00000516527.1
chr3 179879674 179879765 - ENST00000364952.1
chr3 181540660 181540778 - ENST00000362969.1
chr3 182976088 182976204 - ENST00000365632.1
chr4 8394742 8394851 + ENST00000365184.1
chr4 9412904 9412979 - ENST00000516498.1
chr4 9794375 9794485 - ENST00000516193.1
chr4 10117380 10117508 - ENST00000411154.1
chr4 11415675 11415784 - ENST00000410250.1
chr4 19183437 19183479 - ENST00000516007.1
chr4 38760412 38760513 - ENST00000410298.1
chr4 39938373 39938475 + ENST00000517161.1
chr4 40992171 40992290 + ENST00000364866.1
chr4 56963556 56963670 + ENST00000363871.1
chr4 57197343 57197383 - ENST00000516014.1
chr4 72625235 72625333 - ENST00000410304.1
chr4 94741322 94741431 + ENST00000516533.1
chr4 148666454 148666568 - ENST00000517142.1
chr4 149479099 149479200 + ENST00000364976.1
chr4 150828712 150828827 + ENST00000365461.1
chr4 151891823 151891934 - ENST00000516642.1
chr4 152892649 152892765 - ENST00000517268.1
chr4 166974339 166974439 - ENST00000517150.1
chr4 167839515 167839629 - ENST00000391071.1
chr4 178378265 178378382 - ENST00000365061.1
chr4 179327849 179327984 + ENST00000364857.1
chr4 190936293 190936410 + ENST00000362702.1
chr4 190938851 190938969 + ENST00000364275.1
chr5 7047340 7047449 + ENST00000390956.1
chr5 9761019 9761125 + ENST00000410122.1
chr5 16033338 16033465 - ENST00000410380.1
chr5 16854103 16854223 + ENST00000517284.1
chr5 17157080 17157180 - ENST00000516181.1
chr5 36485445 36485542 + ENST00000410246.1
chr5 51182522 51182603 + ENST00000516064.1
chr5 55073297 55073415 + ENST00000362452.1
chr5 55442566 55442673 - ENST00000411071.1
chr5 55556160 55556273 - ENST00000390963.1
chr5 75387533 75387626 - ENST00000517024.1
chr5 87570075 87570193 - ENST00000384400.1
chr5 101466711 101466839 - ENST00000362916.1
chr5 105258695 105258809 - ENST00000364920.1
chr5 118781411 118781528 + ENST00000365222.1
chr5 129450102 129450203 + ENST00000362585.1
chr5 132184269 132184388 + ENST00000364404.1
chr5 136304889 136304995 - ENST00000410353.1
chr5 138348018 138348130 + ENST00000364662.1
chr5 138635541 138635657 + ENST00000362675.1
chr5 145965662 145965763 - ENST00000516984.1
chr5 150857020 150857138 - ENST00000363357.1
chr5 151255127 151255253 - ENST00000410376.1
chr5 155272447 155272538 + ENST00000363405.1
chr5 172719520 172719622 - ENST00000516360.1
chr6 3088920 3089043 - ENST00000410316.1
chr6 4428197 4428315 + ENST00000364315.1
chr6 10753024 10753159 - ENST00000410451.1
chr6 17722017 17722134 - ENST00000364545.1
chr6 19438514 19438649 + ENST00000364653.1
chr6 32046285 32046405 - ENST00000516703.1
chr6 41207258 41207364 - ENST00000390874.1
chr6 68177124 68177201 - ENST00000516156.1
chr6 76574956 76575052 - ENST00000411237.1
chr6 82331917 82332036 + ENST00000391034.1
chr6 106897256 106897372 + ENST00000365516.1
chr6 108573605 108573711 + ENST00000391223.1
chr6 114541845 114541950 - ENST00000391031.1
chr6 117381845 117381962 + ENST00000363378.1
chr6 121007767 121007888 + ENST00000363440.1
chr6 126300958 126301080 - ENST00000516111.1
chr6 127639028 127639118 - ENST00000515959.1
chr6 134578173 134578281 + ENST00000363188.1
chr6 136951381 136951493 + ENST00000390940.1
chr6 140479728 140479831 - ENST00000516298.1
chr6 143770946 143771048 + ENST00000411271.1
chr6 146661556 146661660 + ENST00000411039.1
chr6 152731410 152731529 + ENST00000365174.1
chr6 153480355 153480480 - ENST00000365069.1
chr6 153741573 153741707 + ENST00000410874.1
chr6 165823051 165823165 + ENST00000362653.1
chr7 22338213 22338325 + ENST00000516184.1
chr7 24172324 24172456 + ENST00000516232.1
chr7 33217352 33217450 + ENST00000410809.1
chr7 44165351 44165472 - ENST00000517039.1
chr7 68188898 68189035 - ENST00000410496.1
chr7 71378723 71378841 - ENST00000364144.1
chr7 73901758 73901870 - ENST00000459153.1
chr7 79283425 79283543 + ENST00000363916.1
chr7 82647214 82647327 + ENST00000365411.1
chr7 106422046 106422161 - ENST00000516169.1
chr7 111593708 111593820 - ENST00000410414.1
chr7 114253842 114253961 - ENST00000365464.1
chr7 116584340 116584468 - ENST00000410218.1
chr7 120621480 120621607 - ENST00000365355.1
chr7 120723754 120723867 - ENST00000391326.1
chr7 128337493 128337610 + ENST00000364171.1
chr7 128337764 128337798 + ENST00000517057.1
chr7 129396106 129396217 + ENST00000390936.1
chr7 129667117 129667237 + ENST00000364239.1
chr7 130287672 130287790 - ENST00000458909.1
chr7 140070241 140070345 + ENST00000411181.1
chr7 140086581 140086707 - ENST00000365602.1
chr7 147546976 147547074 + ENST00000516127.1
chr7 152290058 152290176 - ENST00000362534.1
chr8 3558014 3558150 + ENST00000410614.1
chr8 10544079 10544197 + ENST00000391131.1
chr8 11944905 11944954 - ENST00000516220.1
chr8 12191153 12191202 - ENST00000516726.1
chr8 13393538 13393644 + ENST00000516370.1
chr8 17605627 17605739 + ENST00000390978.1
chr8 25994396 25994514 + ENST00000362750.1
chr8 28387928 28388036 + ENST00000365541.1
chr8 28906011 28906121 - ENST00000363849.1
chr8 31455615 31455720 - ENST00000410536.1
chr8 32049544 32049669 - ENST00000516452.1
chr8 32114012 32114139 + ENST00000363376.1
chr8 36621963 36622069 + ENST00000363115.1
chr8 56657791 56657901 + ENST00000411023.1
chr8 58039214 58039321 - ENST00000410273.1
chr8 60368444 60368569 + ENST00000364893.1
chr8 68011537 68011660 + ENST00000516828.1
chr8 69607878 69608014 + ENST00000459032.1
chr8 70842140 70842257 + ENST00000411361.1
chr8 73269963 73270050 + ENST00000516700.1
chr8 89408666 89408776 - ENST00000516095.1
chr8 91523356 91523468 + ENST00000362484.1
chr8 94453505 94453612 + ENST00000410484.1
chr8 108896722 108896839 + ENST00000363936.1
chr8 117034911 117035004 - ENST00000362580.1
chr8 120903372 120903469 - ENST00000365486.1
chr8 141950661 141950762 + ENST00000517055.1
chr9 1333837 1333953 + ENST00000365513.1
chr9 27198285 27198399 + ENST00000411230.1
chr9 32293556 32293690 + ENST00000516504.1
chr9 34206132 34206239 - ENST00000516355.1
chr9 66458144 66458262 - ENST00000365604.1
chr9 68408924 68409041 + ENST00000384547.1
chr9 74914636 74914754 - ENST00000516619.1
chr9 76365888 76365993 - ENST00000391152.1
chr9 84500411 84500513 + ENST00000516358.1
chr9 97904731 97904823 - ENST00000516075.1
chr9 98667287 98667423 + ENST00000362332.1
chr9 101908122 101908248 - ENST00000517133.1
chr9 106451755 106451859 - ENST00000517222.1
chr9 109606030 109606147 - ENST00000390974.1
chr9 110681147 110681259 - ENST00000410527.1
chr9 111754689 111754849 - ENST00000364357.1
chr9 114173924 114174022 - ENST00000411306.1
chr9 115014538 115014658 + ENST00000362655.1
chr9 130603391 130603501 - ENST00000410523.1
chr10 200771 200883 - ENST00000391029.1
chr10 327955 328065 - ENST00000364991.1
chr10 8698679 8698794 - ENST00000391203.1
chr10 12966679 12966785 - ENST00000391197.1
chr10 13769796 13769916 + ENST00000362537.1
chr10 14705394 14705493 - ENST00000364896.1
chr10 19922612 19922741 - ENST00000516192.1
chr10 23286184 23286287 + ENST00000411199.1
chr10 24929095 24929213 + ENST00000362665.1
chr10 26102740 26102846 - ENST00000411087.1
chr10 26798518 26798633 + ENST00000362863.1
chr10 29163322 29163436 - ENST00000362532.1
chr10 31548528 31548633 + ENST00000516670.1
chr10 46351755 46351870 + ENST00000459084.1
chr10 46742028 46742143 + ENST00000411290.2
chr10 47222341 47222456 + ENST00000517068.1
chr10 48206895 48207010 - ENST00000516945.1
chr10 48931789 48931904 + ENST00000410474.1
chr10 49248476 49248591 + ENST00000516340.1
chr10 51255380 51255495 + ENST00000410168.1
chr10 51739425 51739540 - ENST00000410176.1
chr10 55217957 55218048 + ENST00000516352.1
chr10 70221164 70221282 + ENST00000362768.1
chr10 75466248 75466371 + ENST00000516263.1
chr10 79346807 79346917 + ENST00000362722.1
chr10 87812205 87812323 + ENST00000363617.1
chr10 95270305 95270437 - ENST00000391094.1
chr10 98379133 98379240 + ENST00000365177.1
chr10 108729779 108729908 + ENST00000363756.1
chr10 109221318 109221427 + ENST00000363209.1
chr10 112520900 112521000 + ENST00000362494.1
chr10 127834043 127834151 - ENST00000410808.1
chr11 6038226 6038344 + ENST00000365277.1
chr11 8866810 8866905 + ENST00000517096.1
chr11 13929031 13929137 - ENST00000364986.1
chr11 14156532 14156646 + ENST00000391063.1
chr11 18269936 18270053 - ENST00000363466.1
chr11 18287940 18288057 + ENST00000364825.1
chr11 19423419 19423528 - ENST00000363817.1
chr11 21022427 21022543 - ENST00000364189.1
chr11 21405347 21405455 - ENST00000517007.1
chr11 22709897 22709981 + ENST00000410495.1
chr11 27543152 27543273 - ENST00000390987.1
chr11 47825848 47825954 - ENST00000517132.1
chr11 57217656 57217772 + ENST00000516261.1
chr11 71556242 71556291 - ENST00000517093.1
chr11 73909793 73909899 - ENST00000363779.1
chr11 75645980 75646083 + ENST00000411081.1
chr11 95573181 95573288 - ENST00000410646.1
chr11 96207736 96207856 - ENST00000363541.1
chr11 97528464 97528582 + ENST00000362445.1
chr11 104123307 104123343 + ENST00000516442.1
chr11 108991605 108991713 - ENST00000363743.1
chr11 110910822 110910932 - ENST00000363298.1
chr11 111799124 111799232 + ENST00000459480.1
chr11 124506355 124506488 + ENST00000363408.1
chr12 13593818 13593935 - ENST00000364606.1
chr12 26526531 26526666 - ENST00000391247.1
chr12 28658327 28658461 + ENST00000365317.1
chr12 30459364 30459457 - ENST00000515972.1
chr12 34358634 34358752 + ENST00000607318.1
chr12 38555268 38555384 - ENST00000362973.1
chr12 38557205 38557317 - ENST00000364838.1
chr12 42052478 42052595 + ENST00000516555.1
chr12 45511554 45511671 + ENST00000362686.1
chr12 66460001 66460118 + ENST00000516048.1
chr12 80272085 80272199 - ENST00000365072.1
chr12 88445478 88445555 + ENST00000516938.1
chr12 90120713 90120819 + ENST00000516398.1
chr12 99477561 99477683 - ENST00000365454.1
chr12 101866117 101866234 + ENST00000516557.1
chr12 102173592 102173707 + ENST00000364298.1
chr12 102230598 102230705 + ENST00000411114.1
chr12 104519014 104519134 + ENST00000362545.1
chr12 107880288 107880412 - ENST00000410370.1
chr12 109497791 109497905 + ENST00000390836.1
chr12 111777331 111777425 + ENST00000517271.1
chr12 119267486 119267610 + ENST00000362939.1
chr12 123767463 123767581 - ENST00000362975.1
chr12 131784185 131784296 - ENST00000390949.1
chr12 132145608 132145719 + ENST00000390852.1
chr12 132285860 132285979 - ENST00000363646.1
chr12 133300531 133300643 - ENST00000364599.1
chr13 19662627 19662721 + ENST00000516478.1
chr13 21943929 21944038 - ENST00000410815.1
chr13 38428989 38429107 - ENST00000362406.1
chr13 46125620 46125738 - ENST00000363839.1
chr13 51387124 51387242 - ENST00000363841.1
chr13 51601883 51601988 - ENST00000410988.1
chr13 58565484 58565598 + ENST00000365552.1
chr13 61187742 61187868 + ENST00000411144.1
chr13 72552226 72552344 + ENST00000363167.1
chr13 79963669 79963766 - ENST00000516687.1
chr13 90787966 90788095 - ENST00000516887.1
chr13 94677724 94677852 - ENST00000391257.1
chr13 95303651 95303783 - ENST00000410197.1
chr13 98015226 98015355 - ENST00000365420.1
chr13 106807721 106807839 - ENST00000410750.1
chr13 108953560 108953679 - ENST00000411245.1
chr14 20558289 20558386 + ENST00000517190.1
chr14 20614276 20614314 - ENST00000516076.1
chr14 20883146 20883257 + ENST00000363355.1
chr14 24627812 24627931 + ENST00000362934.1
chr14 50019351 50019466 + ENST00000516615.1
chr14 52159470 52159579 + ENST00000515947.1
chr14 68123822 68123928 - ENST00000607639.1
chr14 76070516 76070621 + ENST00000364226.1
chr14 78644146 78644264 - ENST00000362584.1
chr14 107092677 107092791 + ENST00000362610.1
chr15 25983655 25983767 + ENST00000410191.1
chr15 27525465 27525583 - ENST00000363456.1
chr15 40623738 40623849 - ENST00000516905.1
chr15 42144111 42144227 - ENST00000363423.1
chr15 50274640 50274758 + ENST00000364216.1
chr15 50755578 50755695 + ENST00000516567.1
chr15 59866302 59866421 - ENST00000364834.1
chr15 61028968 61029085 + ENST00000391323.1
chr15 69659924 69660020 + ENST00000517163.1
chr15 72150911 72151027 + ENST00000364003.1
chr15 86681500 86681610 - ENST00000517155.1
chr15 98015356 98015482 - ENST00000515920.1
chr15 100614286 100614395 - ENST00000517148.1
chr16 9658247 9658354 - ENST00000363598.1
chr16 9693954 9694085 + ENST00000517118.1
chr16 26040233 26040346 + ENST00000363059.1
chr16 33965426 33965577 + ENST00000363564.1
chr16 34968764 34968875 + ENST00000516106.1
chr16 34969010 34969119 + ENST00000410275.1
chr16 34969743 34969842 + ENST00000516115.1
chr16 34969996 34970104 + ENST00000516815.1
chr16 34980360 34980465 + ENST00000516285.1
chr16 34981403 34981511 + ENST00000516373.1
chr16 34984432 34984546 + ENST00000517246.1
chr16 34985945 34986055 + ENST00000516838.1
chr16 34986199 34986306 + ENST00000516459.1
chr16 34987197 34987313 + ENST00000515951.1
chr16 34988167 34988301 + ENST00000515908.1
chr16 34988417 34988553 + ENST00000516997.1
chr16 34988926 34989059 + ENST00000516864.1
chr16 34989294 34989404 + ENST00000516778.1
chr16 34989548 34989656 + ENST00000517127.1
chr16 47484258 47484372 - ENST00000390988.1
chr16 47539343 47539454 + ENST00000410336.1
chr16 50903366 50903486 - ENST00000362901.1
chr16 53371365 53371483 + ENST00000365323.1
chr16 66335712 66335843 + ENST00000365129.1
chr16 68776383 68776491 + ENST00000363688.1
chr16 75894946 75895055 - ENST00000362429.1
chr16 79298351 79298470 + ENST00000410312.1
chr16 84073523 84073638 - ENST00000362480.1
chr16 84296421 84296534 - ENST00000364491.1
chr17 3960050 3960170 - ENST00000516647.1
chr17 6504264 6504371 - ENST00000364044.1
chr17 15685655 15685769 + ENST00000516020.1
chr17 30290824 30290952 - ENST00000517249.1
chr17 32447075 32447186 - ENST00000516561.1
chr17 34847043 34847166 - ENST00000517103.1
chr17 36888055 36888173 - ENST00000363245.1
chr17 38530341 38530428 + ENST00000516809.1
chr17 39874406 39874512 + ENST00000365050.1
chr17 43404732 43404863 - ENST00000363083.1
chr17 64263861 64263966 + ENST00000516844.1
chr17 64635387 64635501 + ENST00000515889.1
chr17 64891608 64891689 + ENST00000515955.1
chr17 65264226 65264344 + ENST00000363749.1
chr17 72413733 72413843 - ENST00000363151.1
chr18 9844714 9844843 - ENST00000516871.1
chr18 9923917 9924018 + ENST00000411206.1
chr18 19508946 19509055 - ENST00000410588.1
chr18 21750469 21750587 - ENST00000363004.1
chr18 29756013 29756131 - ENST00000362503.1
chr18 39850554 39850680 + ENST00000517231.1
chr18 41651548 41651666 + ENST00000365190.1
chr18 46001858 46001971 - ENST00000364002.1
chr18 47472636 47472759 - ENST00000363657.1
chr18 47845372 47845490 + ENST00000516188.1
chr18 52813777 52813876 - ENST00000516628.1
chr18 70419187 70419286 + ENST00000516789.1
chr18 75575420 75575523 - ENST00000516451.1
chr19 453134 453245 + ENST00000516730.1
chr19 7951862 7951981 - ENST00000363030.1
chr19 12107624 12107731 + ENST00000516251.1
chr19 12138728 12138836 - ENST00000391195.1
chr19 12180979 12181086 + ENST00000516737.1
chr19 12217312 12217429 + ENST00000391274.1
chr19 18082834 18082926 + ENST00000516782.1
chr19 21295934 21296042 - ENST00000364165.1
chr19 24187160 24187309 - ENST00000365096.1
chr19 29492577 29492682 + ENST00000516463.1
chr19 32146262 32146367 - ENST00000516971.1
chr19 32734871 32734989 - ENST00000363868.1
chr19 58874805 58874929 + ENST00000516402.1
chr20 5079033 5079122 - ENST00000391234.1
chr20 5326652 5326806 - ENST00000363443.1
chr20 15261410 15261519 - ENST00000410568.1
chr20 18414486 18414588 + ENST00000516613.1
chr20 21119597 21119715 - ENST00000362639.1
chr20 23141494 23141608 - ENST00000364657.1
chr20 23361533 23361649 - ENST00000364858.1
chr20 29944673 29944781 + ENST00000516840.1
chr20 30596154 30596275 + ENST00000516814.1
chr20 30638391 30638508 + ENST00000391269.1
chr20 33783109 33783226 + ENST00000363431.1
chr20 39482759 39482869 - ENST00000458857.1
chr20 44188397 44188515 - ENST00000365053.1
chr20 46501935 46502017 + ENST00000515961.1
chr20 54780108 54780229 - ENST00000410186.1
chr21 15443192 15443307 + ENST00000364942.1
chr21 26574521 26574629 + ENST00000410986.2
chr21 33935385 33935520 + ENST00000517141.1
chr21 38224211 38224328 + ENST00000362936.1
chr21 43641283 43641396 + ENST00000411330.1
chr22 22146723 22146813 + ENST00000364115.1
chr22 26111008 26111136 - ENST00000410653.1
chr22 26786633 26786742 - ENST00000516458.1
chr22 31701390 31701498 + ENST00000391240.1
chr22 33031088 33031184 - ENST00000516081.1
chrX 1419149 1419268 - ENST00000411342.1
chrX 9101869 9101987 + ENST00000363982.1
chrX 29000969 29001087 - ENST00000364486.1
chrX 32120182 32120293 + ENST00000410990.1
chrX 41152051 41152169 + ENST00000362694.1
chrX 48065693 48065809 + ENST00000517047.1
chrX 52694281 52694397 + ENST00000410676.1
chrX 53935488 53935595 + ENST00000364748.1
chrX 68892323 68892441 + ENST00000606950.1
chrX 69472892 69473012 + ENST00000363603.1
chrX 75875410 75875528 - ENST00000411327.1
chrX 76287130 76287248 + ENST00000364577.1
chrX 94837063 94837161 + ENST00000364697.1
chrX 103105726 103105840 - ENST00000410487.1
chrX 110913057 110913176 - ENST00000364550.1
chrX 128570507 128570624 - ENST00000364648.1
chrX 131072874 131072984 - ENST00000363717.1
chrX 134562093 134562210 - ENST00000364570.1
chrX 141498839 141498957 + ENST00000364130.1
chrX 145508974 145509090 - ENST00000364724.1
chrX 147089620 147089735 - ENST00000364415.1
chrX 150194767 150194878 - ENST00000391293.1
chrY 1369149 1369268 - ENSTR0000411342.1
chrY 9928019 9928137 - ENST00000515957.1
chrY 9930484 9930602 - ENST00000516480.1
chrY 10037764 10037915 + ENST00000515896.1
chrY 19669744 19669856 + ENST00000516506.1
chrY 19671654 19671769 + ENST00000516203.1
chrY 20508009 20508124 - ENST00000516144.1
chrY 20509921 20510033 - ENST00000516858.1
#!/usr/bin/env bash
# make_rRNA.sh
# Kamil Slowikowski
# December 10, 2014
#
# 1. Download chromosome sizes from UCSC if needed.
# 2. Make an interval_list file suitable for CollectRnaSeqMetrics.jar.
#
# Gencode v19 genes:
#
# ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
#
# Picard Tools CollectRnaSeqMetrics.jar:
#
# https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics
# 1. Chromosome sizes from the UCSC genome browser ---------------------------
chrom_sizes=hg19.chrom.sizes
if [[ ! -s $chrom_sizes ]]
then
mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
"SELECT chrom,size FROM chromInfo ORDER BY size DESC;" hg19 \
> $chrom_sizes
fi
# 2. rRNA interval_list file -------------------------------------------------
# Genes from Gencode.
genes=gencode.v19.annotation.gtf
# Output file suitable for Picard CollectRnaSeqMetrics.jar.
rRNA=gencode.v19.rRNA.interval_list
# Header line.
echo '@HD VN:1.0 SO:coordinate' > $rRNA
# Sequence names and lengths.
perl -lane 'print "\@SQ SN:$F[0] LN:$F[1] AS:hg19"' $chrom_sizes | \
grep -v _ \
>> $rRNA
# Intervals for rRNA transcripts.
grep 'gene_type "rRNA"' $genes | \
awk '$3 == "transcript"' | \
cut -f1,4,5,7,9 | \
perl -lane '
/transcript_id "([^"]+)"/ or die "no transcript_id on $.";
print join "\t", (@F[0,1,2,3], $1)
' | \
sort -k1V -k2n -k3n \
>> $rRNA
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