Ns126:Heyn2016

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Background[edit]

  • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
  • https://www.ncbi.nlm.nih.gov/pubmed/26497311
  • WGBS by 101 bp pair-end sequencing.
  • Phred Score: 33
  • 11 primary tumor tissue, 2 metastasis tissue and 9 normal tissues

Method and Procedure[edit]

Sample[edit]

Title geo_accession organism_ch1 treatment_protocol_ch1 description.1 data_processing relation MF
GSM1279516 Brain_white matter Normal sample type: Primary Brain_W SRX381706 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279516/GSM1279516_CpGcontext.Brain_W.txt.gz
GSM1279517 Breast_normal Normal sample type: Primary Breast SRX381631 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279517/GSM1279517_CpGcontext.Breast.txt.gz
GSM1279518 Blood_B-cells_CD19 Normal sample type: Primary CD19 SRX381725 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279518/GSM1279518_CpGcontext.CD19.txt.gz
GSM1279519 Colon_normal Normal sample type: Primary Colon SRX381553 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279519/GSM1279519_CpGcontext.Colon.txt.gz
GSM1279520 Colon_metastasis Metastasis sample type: Primary Colon_M SRX381585 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279520/GSM1279520_CpGcontext.Colon_M.txt.gz
GSM1279521 Colon_cancer Cancer sample type: Primary Colon_P SRX381569 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279521/GSM1279521_CpGcontext.Colon_P.txt.gz
GSM1279522 Lung_H1437 Adenocarcinoma sample type: Cell line H1437 SRX381716 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279522/GSM1279522_CpGcontext.H1437.txt.gz
GSM1279523 Lung_H157 Squamous cell cancer sample type: Cell line H157 SRX381719 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279523/GSM1279523_CpGcontext.H157.txt.gz
GSM1279524 Lung_H1672 Small cell lung cancer sample type: Cell line H1672 SRX381722 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279524/GSM1279524_CpGcontext.H1672.txt.gz
GSM1279527 Lung_normali Normal sample type: Primary Lung SRX381713 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279527/GSM1279527_CpGcontext.Lung.txt.gz
GSM1279532 Brain_U87MG Glioma sample type: Cell line U87MG SRX381701 Bisulfite-Seq ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/supplementary/samples/GSM1279nnn/GSM1279532/GSM1279532_CpGcontext.U87MG.txt.gz
  • Table 2.
File title geo_accession status organism_ch1 treatment_protocol_ch1 description.1 data_processing
GSM1279516_CpGcontext.Brain_W.txt.gz GSM1279516 Brain_white matter GSM1279516 Normal sample type: Primary Brain_WNT SRX381706
GSM1279517_CpGcontext.Breast.txt.gz GSM1279517 Breast_normal GSM1279517 Normal sample type: Primary Breast_NT SRX381631
GSM1279518_CpGcontext.CD19.txt.gz GSM1279518 Blood_B-cells_CD19 GSM1279518 Normal sample type: Primary CD19_NT SRX381725
GSM1279519_CpGcontext.Colon.txt.gz GSM1279519 Colon_normal GSM1279519 Normal sample type: Primary Colon_NT SRX381553
GSM1279520_CpGcontext.Colon_M.txt.gz GSM1279520 Colon_metastasis GSM1279520 Metastasis sample type: Primary Colon_MC SRX381585
GSM1279521_CpGcontext.Colon_P.txt.gz GSM1279521 Colon_cancer GSM1279521 Cancer sample type: Primary Colon_PC SRX381569
GSM1279522_CpGcontext.H1437.txt.gz GSM1279522 Lung_H1437 GSM1279522 Adenocarcinoma sample type: Cell line H1437_LCC SRX381716
GSM1279523_CpGcontext.H157.txt.gz GSM1279523 Lung_H157 GSM1279523 Squamous cell cancer sample type: Cell line H157_LCC SRX381719
GSM1279524_CpGcontext.H1672.txt.gz GSM1279524 Lung_H1672 GSM1279524 Small cell lung cancer sample type: Cell line H1672_LCC SRX381722
GSM1279527_CpGcontext.Lung.txt.gz GSM1279527 Lung_normali GSM1279527 Normal sample type: Primary Lung_NT SRX381713
GSM1279532_CpGcontext.U87MG.txt.gz GSM1279532 Brain_U87MG GSM1279532 Glioma sample type: Cell line U87MG_BC SRX381701`

SRA Download[edit]

SRA to Fastq[edit]

wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381553
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381569
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381585
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381601
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381611
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381621
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381631
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381646
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381661
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381666
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381671
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381678
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381693
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381697
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381701
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381706
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381710
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381713
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381716
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381719
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381722
wget -r -nd ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/SRX381725

trim_glore[edit]

Fastq to Bam[edit]

Sample N(reads) N(mapped) P(mapping) N(C) N(MCPG) N(MCHG) N(MCHH) N(UCPG) N(UCHG) N(UCHH) P(MCPG) P(MCHG) P(MCHH)
SRR1035722_1 36231449 26356409 72.7% 992806465 56929401 665378 1462755 24444494 281230022 628074415 70.0% 0.2% 0.2%
SRR1035723_1 38672444 28821090 74.5% 1093399553 63203116 573053 1246437 27172725 309871245 691332977 69.9% 0.2% 0.2%
SRR1035724_1 38169545 28474993 74.6% 1078721744 62354261 576320 1254164 26757183 305665500 682114316 70.0% 0.2% 0.2%
SRR1035725_1 35676108 26566972 74.5% 1019460690 60060766 502315 1114013 26113507 289896735 641773354 69.7% 0.2% 0.2%
SRR1035726_1 42115048 31984957 75.9% 1213271012 70615619 707726 1468673 29983057 343628632 766867305 70.2% 0.2% 0.2%
SRR1035727_1 42756295 32415649 75.8% 1227727881 71552761 716711 1484636 30188318 347670963 776114492 70.3% 0.2% 0.2%
SRR1035728_1 42411383 32186391 75.9% 1220313570 71002070 724203 1493462 30218679 345662242 771212914 70.1% 0.2% 0.2%
SRR1035729_1 42623243 32307805 75.8% 1223735711 71070930 718040 1481741 30319685 346663966 773481349 70.1% 0.2% 0.2%
SRR1035730_1 42047512 31854981 75.8% 1206042893 70201432 742769 1511214 29815343 341471569 762300566 70.2% 0.2% 0.2%
SRR1035731_1 42403142 32112901 75.7% 1215614793 70706477 725488 1482816 30013259 344211647 768475106 70.2% 0.2% 0.2%
SRR1035732_1 33362690 24707272 74.1% 941095281 55251654 457269 1019789 23501401 267177061 593688107 70.2% 0.2% 0.2%
SRR1035733_1 33381741 24709065 74.0% 941288700 55277191 455919 1016786 23547047 267294566 593697191 70.1% 0.2% 0.2%
SRR1035734_1 33196884 24571704 74.0% 936212940 54864931 451643 1005279 23520896 265896154 590474037 70.0% 0.2% 0.2%
SRR1035735_1 33985218 25130974 73.9% 956402792 55943101 474478 1057439 24011066 271578107 603338601 70.0% 0.2% 0.2%
SRR1035736_1 33887645 25047606 73.9% 952060048 55686131 457557 1021131 23788426 270227147 600879656 70.1% 0.2% 0.2%
SRR1035737_1 33354700 24650161 73.9% 936151932 54670947 455043 1013284 23463753 265750296 590798609 70.0% 0.2% 0.2%
SRR1035738_1 40126453 31958454 79.6% 1170141034 54984718 720678 1774947 27387084 313488867 771784740 66.8% 0.2% 0.2%
SRR1035739_1 42630446 34724930 81.5% 1280677712 60798490 611014 1482864 30244382 343441526 844099436 66.8% 0.2% 0.2%
SRR1035740_1 42154379 34384348 81.6% 1266363559 60128458 613867 1500954 29880923 339603738 834635619 66.8% 0.2% 0.2%
SRR1035741_1 39992910 32461489 81.2% 1211429605 58662506 543038 1348799 29379031 326181180 795315051 66.6% 0.2% 0.2%
SRR1035742_1 46418632 38547447 83.0% 1420008578 67810264 759476 1759239 33343955 380559074 935776570 67.0% 0.2% 0.2%
SRR1035743_1 47276691 39199235 82.9% 1441569094 68899681 769964 1782273 33700891 386228454 950187831 67.2% 0.2% 0.2%
SRR1035744_1 46542012 38617083 83.0% 1421723100 67864941 776755 1779701 33458732 381130422 936712549 67.0% 0.2% 0.2%
SRR1035745_1 46843070 38812333 82.9% 1427699210 68060537 765033 1764230 33641134 382643861 940824415 66.9% 0.2% 0.2%
SRR1035746_1 46170806 38253135 82.9% 1406415812 67159539 796772 1804119 33062801 376849829 926742752 67.0% 0.2% 0.2%
SRR1035747_1 46544502 38538932 82.8% 1416472851 67597445 776087 1766890 33272512 379517129 933542788 67.0% 0.2% 0.2%
SRR1035748_1 36600721 29621066 80.9% 1096324957 52954395 483095 1207263 25998029 294582645 721099530 67.1% 0.2% 0.2%
SRR1035749_1 36640873 29622158 80.8% 1096474862 53014044 482206 1209477 26061564 294618682 721088889 67.0% 0.2% 0.2%
SRR1035750_1 36418326 29437479 80.8% 1090003740 52580173 477676 1194376 25991217 292993343 716766955 66.9% 0.2% 0.2%
SRR1035751_1 37283288 30097060 80.7% 1113232015 53583454 501012 1258616 26503728 299184745 732200460 66.9% 0.2% 0.2%
SRR1035752_1 37060706 29929057 80.8% 1105518374 53252901 482131 1206278 26213632 296987990 727375442 67.0% 0.2% 0.2%
SRR1035753_1 36524684 29497226 80.8% 1088783934 52383715 480767 1201878 25891164 292553540 716272870 66.9% 0.2% 0.2%
SRR1035754_1 44374421 35641925 80.3% 1297737027 56550048 783384 1928227 33889478 345634464 858951426 62.5% 0.2% 0.2%
SRR1035755_1 47123418 38686887 82.1% 1418615508 62395744 657788 1600283 37310750 378205898 938445045 62.6% 0.2% 0.2%
SRR1035756_1 46494325 38200717 82.2% 1398750194 61544370 665506 1620058 36755277 372805600 925359383 62.6% 0.2% 0.2%
SRR1035757_1 33757685 27558529 81.6% 1022678995 45970453 447518 1108988 27503711 273698575 673949750 62.6% 0.2% 0.2%
SRR1035758_1 51672955 43202041 83.6% 1581348447 69853985 822137 1902495 41435007 421408587 1045926236 62.8% 0.2% 0.2%
SRR1035759_1 52552541 43875424 83.5% 1603622609 70893193 835216 1927920 41918303 427271471 1060776506 62.8% 0.2% 0.2%
SRR1035760_1 52028953 43462815 83.5% 1590035355 70151952 843868 1933038 41772663 423787545 1051546289 62.7% 0.2% 0.2%
SRR1035761_1 52203954 43546727 83.4% 1591628706 70115005 830864 1912659 41792593 424214663 1052762922 62.7% 0.2% 0.2%
SRR1035762_1 51432756 42899477 83.4% 1567397860 69243147 863158 1954416 41097046 417613231 1036626862 62.8% 0.2% 0.2%
SRR1035763_1 51936573 43290148 83.4% 1581519608 69783508 841838 1914746 41424608 421377354 1046177554 62.8% 0.2% 0.2%
SRR1035764_1 41020260 33330224 81.3% 1226993280 54818173 527463 1312101 32420376 327658331 810256836 62.8% 0.2% 0.2%
SRR1035765_1 41052812 33343513 81.2% 1227624175 54908911 528111 1315673 32457666 327941036 810472778 62.8% 0.2% 0.2%
SRR1035766_1 40712660 33053039 81.2% 1217077676 54307682 521433 1297309 32298209 325186448 803466595 62.7% 0.2% 0.2%
SRR1035767_1 41671785 33805763 81.1% 1243572762 55361566 547813 1367520 32949551 332187811 821158501 62.7% 0.2% 0.2%
SRR1035768_1 41503242 33656899 81.1% 1236709139 55086643 526393 1311440 32663075 330230911 816890677 62.8% 0.2% 0.2%
SRR1035769_1 40892220 33159591 81.1% 1217419991 54160359 524999 1309045 32229531 325131538 804064519 62.7% 0.2% 0.2%
SRR1035770_1 46520916 36005366 77.4% 1303239008 47706437 392006 922516 39617310 343379869 871220870 54.6% 0.1% 0.1%
SRR1035771_1 46414984 36467622 78.6% 1321978264 48246698 365161 857484 40128827 348027507 884352587 54.6% 0.1% 0.1%
SRR1035772_1 46698438 36931175 79.1% 1343232054 49132879 370344 880527 40949341 353897862 898001101 54.5% 0.1% 0.1%
SRR1035773_1 44515227 36654877 82.3% 1335559941 49108711 338401 827107 40003144 350823734 894458844 55.1% 0.1% 0.1%
SRR1035774_1 47498272 38925077 82.0% 1422251250 52656528 360868 883508 42309888 373729030 952311428 55.4% 0.1% 0.1%
SRR1035775_1 47993625 39338205 82.0% 1428587161 53089619 361541 877516 42993840 376426283 954838362 55.3% 0.1% 0.1%
SRR1035776_1 46745030 38513176 82.4% 1424830729 53136208 371102 891738 43254982 375890471 951286228 55.1% 0.1% 0.1%
SRR1035777_1 45500363 37600702 82.6% 1397191787 52133415 362142 869751 42813494 368728979 932284006 54.9% 0.1% 0.1%
SRR1035778_1 46828689 38624177 82.5% 1427434421 53057220 363400 875142 43281298 376483312 953374049 55.1% 0.1% 0.1%
SRR1035779_1 40595642 33420553 82.3% 1227432100 45961822 340618 819171 37279212 324195235 818836042 55.2% 0.1% 0.1%
SRR1035780_1 62940191 48550487 77.1% 1734872359 67573909 601959 1449099 51775843 456720838 1156750711 56.6% 0.1% 0.1%
SRR1035781_1 61291838 48240404 78.7% 1727526315 67174823 555794 1344948 51445648 454514976 1152490126 56.6% 0.1% 0.1%
SRR1035782_1 63278424 49846622 78.8% 1789904164 69646210 575617 1400533 53466326 471240194 1193575284 56.6% 0.1% 0.1%
SRR1035783_1 58831142 48192822 81.9% 1730415712 68298140 522771 1307048 50748847 454461060 1155077846 57.4% 0.1% 0.1%
SRR1035784_1 63181484 51516939 81.5% 1855959363 73800255 562998 1406647 54088183 487517361 1238583919 57.7% 0.1% 0.1%
SRR1035785_1 63692191 51886308 81.5% 1856778254 74075763 560856 1400302 54675078 488855712 1237210543 57.5% 0.1% 0.1%
SRR1035786_1 62270233 51045276 82.0% 1862011841 74460568 576038 1419385 55386423 491060518 1239108909 57.3% 0.1% 0.1%
SRR1035787_1 61085781 50245446 82.3% 1842819779 73615572 567990 1398985 55370895 486406301 1225460036 57.1% 0.1% 0.1%
SRR1035788_1 62229996 51060158 82.1% 1860220299 74205391 564944 1395963 55241189 490509785 1238303027 57.3% 0.1% 0.1%
SRR1035789_1 57247676 46746488 81.7% 1687728750 67887659 552138 1369009 49936042 445135297 1122848605 57.6% 0.1% 0.1%
SRR1035790_1 60048643 44674883 74.4% 1571276437 53613688 539622 1182691 73282698 441501621 1001156117 42.2% 0.1% 0.1%
SRR1035791_1 60008484 45273430 75.4% 1594750385 54160775 507677 1110960 74281760 447715812 1016973401 42.2% 0.1% 0.1%
SRR1035792_1 60344165 45897611 76.1% 1622389621 55261716 513085 1135739 75759300 455870110 1033849671 42.2% 0.1% 0.1%
SRR1035793_1 56610155 44702916 79.0% 1581558605 54138085 467006 1057369 72917067 443343987 1009635091 42.6% 0.1% 0.1%
SRR1035794_1 60658563 47626463 78.5% 1692216204 58275928 500954 1137191 77623550 474459104 1080219477 42.9% 0.1% 0.1%
SRR1035795_1 61384382 48200861 78.5% 1702156127 58872375 500394 1129634 78928196 478633934 1084091594 42.7% 0.1% 0.1%
SRR1035796_1 59963818 47363964 79.0% 1704764693 59269477 513609 1146552 79466441 479602081 1084766533 42.7% 0.1% 0.1%
SRR1035797_1 58279768 46215257 79.3% 1669602625 58090464 501098 1119650 78285238 469865303 1061740872 42.6% 0.1% 0.1%
SRR1035798_1 60051400 47483827 79.1% 1707250478 59095298 503536 1129531 79491057 480179307 1086851749 42.6% 0.1% 0.1%
SRR1035799_1 52596761 41408272 78.7% 1476759415 51741276 475451 1059853 68681101 415804928 938996806 43.0% 0.1% 0.1%
SRR1035800_1 40106268 31755232 79.2% 1137641163 49033401 726877 2266471 18271317 288229242 779113855 72.9% 0.3% 0.3%
SRR1035801_1 38488024 30360140 78.9% 1088832548 47122295 705745 2193100 17417558 275958029 745435821 73.0% 0.3% 0.3%
SRR1035802_1 38314917 30299854 79.1% 1086660774 47052939 697771 2174800 17422712 275409059 743903493 73.0% 0.3% 0.3%
SRR1035803_1 41585835 34657144 83.3% 1242182200 53933305 789582 2497526 19538143 313445365 851978279 73.4% 0.3% 0.3%
SRR1035804_1 41907709 35044721 83.6% 1264818547 55301550 801023 2533452 19972408 319645040 866565074 73.5% 0.2% 0.3%
SRR1035805_1 42481868 35583563 83.8% 1283786245 56213416 854843 2683701 20250977 324547019 879236289 73.5% 0.3% 0.3%
SRR1035806_1 40154762 33255816 82.8% 1203935588 52780268 768977 2428273 18703797 304277613 824976660 73.8% 0.3% 0.3%
SRR1035807_1 40597084 33087865 81.5% 1184899980 50934561 759356 2389428 18651498 299618859 812546278 73.2% 0.3% 0.3%
SRR1035808_1 40186019 32908838 81.9% 1178071557 50477627 750164 2358661 18690022 297951699 807843384 73.0% 0.3% 0.3%
SRR1035809_1 40623459 33250740 81.9% 1190390779 51076376 761925 2389986 18942922 301164479 816055091 72.9% 0.3% 0.3%
SRR1035810_1 39990834 32610579 81.5% 1163733467 49568904 748160 2353128 18469505 294189949 798403821 72.9% 0.3% 0.3%
SRR1035811_1 37687878 30499485 80.9% 1121777555 50148392 754018 2324423 18159177 285469294 764922251 73.4% 0.3% 0.3%
SRR1035812_1 37092815 29651290 79.9% 1091281965 48686971 736013 2270028 17659645 277746958 744182350 73.4% 0.3% 0.3%
SRR1035813_1 37006842 29880538 80.7% 1101657858 49209692 728399 2250422 17946954 280517101 751005290 73.3% 0.3% 0.3%
SRR1035814_1 42536480 35583514 83.7% 1285295375 56892581 819512 2573566 20537273 326018226 878454217 73.5% 0.3% 0.3%
SRR1035815_1 47913251 37367213 78.0% 1351568540 56510811 610876 1776322 19489614 330817875 942363042 74.4% 0.2% 0.2%
SRR1035816_1 45586019 35438612 77.7% 1283367630 53930902 591780 1712493 18455154 314245763 894431538 74.5% 0.2% 0.2%
SRR1035817_1 45422738 35373259 77.9% 1280644485 53790475 584536 1696771 18425453 313629867 892517383 74.5% 0.2% 0.2%
SRR1035818_1 47604749 39174778 82.3% 1420777243 59969839 634795 1867696 20141667 346582776 991580470 74.9% 0.2% 0.2%
SRR1035819_1 48062450 39675267 82.5% 1448530940 61592989 646608 1896735 20599438 353873765 1009921405 74.9% 0.2% 0.2%
SRR1035820_1 48829014 40370534 82.7% 1473078831 62703742 700167 2058108 20908853 359999045 1026708916 75.0% 0.2% 0.2%
SRR1035821_1 46628485 38099788 81.7% 1395068403 59337067 622464 1830100 19543701 340777142 972957929 75.2% 0.2% 0.2%
SRR1035822_1 46731321 37564817 80.4% 1360008475 56854712 616591 1809244 19306370 332407858 949013700 74.7% 0.2% 0.2%
SRR1035823_1 46424865 37490726 80.8% 1356810843 56552413 609859 1787426 19389028 331625256 946846861 74.5% 0.2% 0.2%
SRR1035824_1 46947416 37892633 80.7% 1371476627 57252705 621179 1815202 19646429 335274448 956866664 74.5% 0.2% 0.2%
SRR1035825_1 46189258 37125640 80.4% 1339566025 55495422 610801 1792929 19182460 327260527 935223886 74.3% 0.2% 0.2%
SRR1035826_1 43605729 34734130 79.7% 1290160854 56160956 625027 1795788 18800554 317469176 895309353 74.9% 0.2% 0.2%
SRR1035827_1 42861727 33688737 78.6% 1252052960 54378357 609255 1755489 18247298 308133949 868928612 74.9% 0.2% 0.2%
SRR1035828_1 43056467 34177392 79.4% 1272164341 55279756 605521 1739457 18652088 313193757 882693762 74.8% 0.2% 0.2%
SRR1035829_1 48984785 40436828 82.5% 1477291324 63627780 664477 1930386 21243121 362337692 1027487868 75.0% 0.2% 0.2%
SRR1035830_1 122387500 96891517 79.2% 3452957650 133743349 992458 2368277 126133211 966568346 2223152009 51.5% 0.1% 0.1%
SRR1035831_1 180936136 145570639 80.5% 5240282995 193217687 1431458 3476566 190379841 1455856420 3395921023 50.4% 0.1% 0.1%
SRR1035832_1 172063603 138391453 80.4% 4959929490 184214947 1376360 3312810 180630617 1379663795 3210730961 50.5% 0.1% 0.1%
SRR1035833_1 178680281 143631742 80.4% 5158597742 192288295 1387654 3368543 187425692 1433913964 3340213594 50.6% 0.1% 0.1%
SRR1035834_1 171844758 136327563 79.3% 4840431463 179394249 1287756 3137604 174068248 1343172401 3139371205 50.8% 0.1% 0.1%
SRR1035835_1 179429223 142409791 79.4% 4894377322 225516712 1543866 4067121 121840525 1336643706 3204765392 64.9% 0.1% 0.1%
SRR1035836_1 176084120 140382021 79.7% 4861035695 225046969 1570647 4114742 122269797 1329137440 3178896100 64.8% 0.1% 0.1%
SRR1035837_1 182109789 144869405 79.6% 5021547782 232044194 1640418 4299062 125718350 1373981079 3283864679 64.9% 0.1% 0.1%
SRR1035838_1 175859200 140614099 80.0% 4901029857 226616594 1567681 4114297 124240917 1342792911 3201697457 64.6% 0.1% 0.1%
SRR1035839_1 157787934 123250898 78.1% 4374242400 204773680 1543512 3918027 116398451 1207633728 2839975002 63.8% 0.1% 0.1%
SRR1035840_1 97824299 80469426 82.3% 2894981772 141005150 3192085 9361119 50638841 754533473 1936251104 73.6% 0.4% 0.5%
SRR1035841_1 100022884 82182965 82.2% 2951581357 143527067 3246952 9547007 51412368 769003867 1974844096 73.6% 0.4% 0.5%
SRR1035842_1 165474210 135822388 82.1% 4802310660 227708222 5179739 15370328 81761651 1242677784 3229612936 73.6% 0.4% 0.5%
SRR1035843_1 178375059 145625083 81.6% 5127069862 240731101 5508578 16444052 86318881 1324573379 3453493871 73.6% 0.4% 0.5%
SRR1035844_1 168215760 137989290 82.0% 4899346338 232492004 5304920 15747213 83613430 1269116986 3293071785 73.5% 0.4% 0.5%
SRR1035845_1 130831169 108279523 82.8% 3918464372 190487688 4305112 12582952 69252470 1021199440 2620636710 73.3% 0.4% 0.5%
SRR1035846_1 155650620 126961137 81.6% 4545809716 217407158 4951261 14574874 79706413 1182662126 3046507884 73.2% 0.4% 0.5%
SRR1035847_1 46402705 37414150 80.6% 1361002175 42529128 442670 1144602 36905700 338937815 941042260 53.5% 0.1% 0.1%
SRR1035848_1 44470848 35755096 80.4% 1302218749 40887927 435056 1123739 35323616 324365567 900082844 53.7% 0.1% 0.1%
SRR1035849_1 44567216 35856939 80.5% 1305576765 40959218 428277 1112381 35409702 325303700 902363487 53.6% 0.1% 0.1%
SRR1035850_1 47702501 40503387 84.9% 1475466276 46451051 468770 1241536 39567728 366037608 1021699583 54.0% 0.1% 0.1%
SRR1035851_1 48130504 41004456 85.2% 1503434684 47696825 475687 1257048 40461779 373590885 1039952460 54.1% 0.1% 0.1%
SRR1035852_1 48774704 41628917 85.3% 1525509197 48503619 529660 1406237 41008049 379228675 1054832957 54.2% 0.1% 0.1%
SRR1035853_1 46209098 38970631 84.3% 1431616918 45434653 456911 1199912 38272114 355605022 990648306 54.3% 0.1% 0.1%
SRR1035854_1 46761580 38856655 83.1% 1414108077 43934203 457182 1203107 38115189 351466112 978932284 53.5% 0.1% 0.1%
SRR1035855_1 46345393 38693434 83.5% 1407878550 43627763 450119 1182287 38076673 349950254 974591454 53.4% 0.1% 0.1%
SRR1035856_1 46860681 39101101 83.4% 1422642997 44146645 459497 1205535 38528576 353704120 984598624 53.4% 0.1% 0.1%
SRR1035857_1 46080860 38299638 83.1% 1389567491 42760898 453102 1196362 37574992 345186737 962395400 53.2% 0.1% 0.1%
SRR1035858_1 43281701 35618472 82.3% 1329238996 43301816 466967 1210378 36358668 332643286 915257881 54.4% 0.1% 0.1%
SRR1035859_1 42695473 34681508 81.2% 1294930862 42060564 458259 1190656 35400769 324082908 891737706 54.3% 0.1% 0.1%
SRR1035860_1 42737999 35060188 82.0% 1311273676 42667840 448514 1156875 35979569 328338326 902682552 54.3% 0.1% 0.1%
SRR1035861_1 48889832 41701373 85.3% 1529623499 49250609 486507 1266616 41512356 381570751 1055536660 54.3% 0.1% 0.1%
SRR1035862_1 43652243 34384472 78.8% 1193708416 50420818 4901337 17102564 16839254 280645348 823799095 75.0% 1.7% 2.0%
SRR1035863_1 78549163 60967800 77.6% 2086186421 88328232 8778013 30528432 29878297 495689528 1432983919 74.7% 1.7% 2.1%
SRR1035864_1 73243529 58027811 79.2% 2004600627 84222213 8211294 28717696 27514223 472357014 1383578187 75.4% 1.7% 2.0%
SRR1035865_1 74457408 57490402 77.2% 1990871735 85148132 8403532 29089891 28187197 471167835 1368875148 75.1% 1.8% 2.1%
SRR1035866_1 72757668 60830122 83.6% 2128051986 76251742 2224331 6264368 40629441 507925801 1494756303 65.2% 0.4% 0.4%
SRR1035867_1 74812203 61984312 82.9% 2136723316 75760071 2228307 6259023 41103187 512824980 1498547748 64.8% 0.4% 0.4%
SRR1035868_1 83486707 69908845 83.7% 2444847012 89915965 2643118 7400396 46548527 587548210 1710790796 65.9% 0.4% 0.4%
SRR1035869_1 41320147 34409470 83.3% 1208339715 46459800 1320247 3579845 24212582 295213850 837553391 65.7% 0.4% 0.4%
SRR1035870_1 47789103 40924532 85.6% 1425544489 46319030 1512034 4071687 36599577 349031146 988011015 55.9% 0.4% 0.4%
SRR1035871_1 61310358 50947605 83.1% 1753501777 55877077 1915502 5118611 45692802 433076875 1211820910 55.0% 0.4% 0.4%
SRR1035872_1 69142773 59266825 85.7% 2085664823 67892559 2234554 6083923 54079900 510788530 1444585357 55.7% 0.4% 0.4%
SRR1035873_1 19183882 16312251 85.0% 567841318 18727861 603633 1625652 14465963 138857946 393560263 56.4% 0.4% 0.4%
SRR1035874_1 78862706 66882077 84.8% 2301759629 75631206 2460088 6584233 59326462 564886601 1592871039 56.0% 0.4% 0.4%
SRR1035875_1 52679182 41593645 79.0% 1434844681 60414839 2626612 8957240 17903363 340338475 1004604152 77.1% 0.8% 0.9%
SRR1035876_1 42830887 33753115 78.8% 1174302962 49719721 2155155 7325554 14800889 279667353 820634290 77.1% 0.8% 0.9%
SRR1035877_1 85498668 66821419 78.2% 2338028492 103484480 4480985 14830338 29742627 570720424 1614769638 77.7% 0.8% 0.9%
SRR1035878_1 95164282 71050862 74.7% 2472481090 109251506 4777013 15492036 33057292 607226785 1702676458 76.8% 0.8% 0.9%
SRR1035879_1 160857256 121844324 75.7% 4387616697 204827680 4165477 11273308 147288362 1249487995 2770573875 58.2% 0.3% 0.4%
SRR1035880_1 162610785 122398416 75.3% 4409289994 205742900 4169412 11297511 148363331 1255642305 2784074535 58.1% 0.3% 0.4%
SRR1035881_1 122178695 91185010 74.6% 3295540452 154931631 3113323 8422807 112007006 939022709 2078042976 58.0% 0.3% 0.4%
SRR1035882_1 118392394 93715052 79.2% 3279344925 131219340 2680794 7854033 45130063 780262948 2312197747 74.4% 0.3% 0.3%
SRR1035883_1 96191682 75468112 78.5% 2631230080 101130016 2156234 6482958 34568940 613453273 1873438659 74.5% 0.4% 0.3%
SRR1035884_1 118745673 91541752 77.1% 3202677064 130072050 2947927 8611131 44239240 761040345 2255766371 74.6% 0.4% 0.4%
SRR1035885_1 74242906 63517801 85.6% 2235564297 67291974 1744210 4646299 70944060 563506266 1527431488 48.7% 0.3% 0.3%
SRR1035886_1 127417108 109304663 85.8% 3861416749 102241861 2930992 8334102 111399368 924600371 2711910055 47.9% 0.3% 0.3%
SRR1035887_1 131669941 112388271 85.4% 4002848671 114341836 2973117 8149999 124720057 994309022 2758354640 47.8% 0.3% 0.3%
SRR1035888_1 86304659 71697120 83.1% 2485016766 62769121 2271845 6206697 87373959 618332059 1708063085 41.8% 0.4% 0.4%
SRR1035889_1 127170770 108342009 85.2% 3846945108 101343359 2805069 7363971 139291584 969400429 2626740696 42.1% 0.3% 0.3%
SRR1035890_1 119854663 101759415 84.9% 3595709881 88725745 2560568 6955439 124142230 880809300 2492516599 41.7% 0.3% 0.3%
SRR1035891_1 91239997 74745248 81.9% 2653614957 108388664 2146269 5526595 59730189 680506327 1797316913 64.5% 0.3% 0.3%
SRR1035892_1 126577102 103852068 82.0% 3629689644 144390800 2934970 7846476 75558554 906300942 2492657902 65.6% 0.3% 0.3%
SRR1035893_1 111871350 93275476 83.4% 3316187159 135223354 2983166 7759640 70107364 844289491 2255824144 65.9% 0.4% 0.3%
SRR1035894_1 140809291 100175988 71.1% 3539413261 144646017 2467134 7141204 44663939 836046240 2504448727 76.4% 0.3% 0.3%
SRR1035895_1 95587884 64890746 67.9% 2251742449 105473176 1989431 5274051 34333784 565817884 1538854123 75.4% 0.4% 0.3%
SRR1035896_1 82314087 54844741 66.6% 1889983707 83000452 1631471 4522452 25774684 461578107 1313476541 76.3% 0.4% 0.3%

Bam to MethylFreq[edit]

#!/bin/csh
#PBS -N MergeCOVbySRX
#PBS -q pdafm
#PBS -l nodes=1:ppn=1
#PBS -l walltime=72:00:00
#PBS -V
#PBS -M shihcheng.guo@gmail.com
#PBS -m abe
#PBS -A k4zhang-group 
cd /home/shg047/oasis/Estellar2016/methyfreq
perl ~/bin/mergeBismarkCovbySRX.pl /home/shg047/oasis/Estellar2016/fastq/SRA112056.txt
  • method 2
cd /home/shg047/oasis/Estellar2016/methyfreq
perl ~/bin/mergeBismarkCovbySRXPBS.pl ../fastq/SRA112056.txt

MF to Wig[edit]

Bam to Hapinfo[edit]

  • Bam File Directory
TSCC-1: /home/ddiep/dinh_working/Bellvitge_BRI_WGBS/methylfiles/BAMfiles
TSCC-2: /oasis/tscc/scratch/ddiep/BAMfiles
Genome-miner:  /media/LTS_60T/Dinh/WGBS_LTS33/Hg19/Estellar_Bellvitge/BAMfiles
  • Bam to hapinfo
cd /oasis/tscc/scratch/ddiep/BAMfiles
perl ~/bin/SaminfoPre4hapinfo.pl > ~/oasis/Estellar2016/SaminfoPre4hapinfo.txt
cd /home/shg047/oasis/Estellar2016/bam
perl ~/bin/bam2hapInfo2PBS.pl ../SaminfoPre4hapinfo.txt submit nonbismark
qsub SRX381621_tumor_breast.chr20.job
  • Merge hapinfo in different chrosome to one file by sample ID
cd /home/shg047/oasis/Estellar2016/hapinfo
perl ~/bin/hapinfoMergeByChrosome.pl
cd /home/shg047/oasis/Estellar2016/mergeHapinfo

Haploinfo to Methylation Haplotype Block (MHB)[edit]

cd /home/shg047/oasis/Estellar2016/mergeHapinfo
cat *.hapInfo.txt >> HapinfoMerge.txt
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.4 > Heyn2016.R0.4.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.5 > Heyn2016.R0.5.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.6 > Heyn2016.R0.6.methyblock.bed
perl ~/bin/hapinfo2mhb.pl HapinfoMerge.txt 0.7 > Heyn2016.R0.7.methyblock.bed
qsub hapinfo2mhb.job
bedtools intersect -wa -u -a ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed -b Heyn2016.R0.5.methyblock.bed | wc -l 
bedtools intersect -wa -u -a Heyn2016.R0.5.methyblock.bed -b ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed | wc -l 
wc -l ../../monod/mhb/WGBS_pooled_mappable_bins.all_autosomes.mld_blocks_r2-0.5.bed
  • 73976 Heyn2016.R0.5.methyblock.bed:File:Heyn2016.R0.5.methyblock.bed.txt
  • 71697 of 147888 within Heyn2016.R0.5.methyblock.bed
  • 73976 of Heyn2016.R0.5.methyblock.bed within 147888
  • MHB identified by Heyn2016 dataset 100% located within our previous defined MHBs

Hapinfo to Methylation frequency(MF)[edit]

perl ~/bin/hapinfo2mf-Estellar.pl ./ > ../Estellar2016.hapinfo2mf.txt

Hapinfo to Methylation Haplotype Load[edit]

cd /home/shg047/oasis/Estellar2016/mergeHapinfo
perl ~/bin/hapinfo2mhl.pl ./ >  Estellar2016.MHL.txt
qsub hapinfo2mhlPBS.job
* Estellar2016.MHL.txt
* 22 samples
* 147314 MHB
* missing ratio: 19.01826%

MHL[edit]