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]
- assemble sample config file
- ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/
- paired-end DNA sequencing (two reads of 100 bp each) using the Illumina HiSeq 2000
- 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: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP033%2FSRP033252
- GEO: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52271
- GEO Download: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52271/suppl/
- GEO Download: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE52nnn/GSE52272/suppl/
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%