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==Background== * 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== ===Sample=== * [[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 {|style="font-size:80%;" |align="left" style="background:#f0f0f0;"|''' Title''' |align="left" style="background:#f0f0f0;"|''' geo_accession''' |align="left" style="background:#f0f0f0;"|''' organism_ch1''' |align="left" style="background:#f0f0f0;"|''' treatment_protocol_ch1''' |align="left" style="background:#f0f0f0;"|''' description.1''' |align="left" style="background:#f0f0f0;"|''' data_processing''' |align="left" style="background:#f0f0f0;"|''' relation''' |align="left" style="background:#f0f0f0;"|''' 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. {|style="font-size:80%;" |align="left" style="background:#f0f0f0;"|''' File''' |align="left" style="background:#f0f0f0;"|''' title''' |align="left" style="background:#f0f0f0;"|''' geo_accession''' |align="left" style="background:#f0f0f0;"|''' status''' |align="left" style="background:#f0f0f0;"|''' organism_ch1''' |align="left" style="background:#f0f0f0;"|''' treatment_protocol_ch1''' |align="left" style="background:#f0f0f0;"|''' description.1''' |align="left" style="background:#f0f0f0;"|''' 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=== * 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=== 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=== === Fastq to Bam === {|style="font-size:80%;" |align="left" style="background:#f0f0f0;"|''' Sample''' |align="left" style="background:#f0f0f0;"|''' N(reads)''' |align="left" style="background:#f0f0f0;"|''' N(mapped)''' |align="left" style="background:#f0f0f0;"|''' P(mapping)''' |align="left" style="background:#f0f0f0;"|''' N(C)''' |align="left" style="background:#f0f0f0;"|''' N(MCPG)''' |align="left" style="background:#f0f0f0;"|''' N(MCHG)''' |align="left" style="background:#f0f0f0;"|''' N(MCHH)''' |align="left" style="background:#f0f0f0;"|''' N(UCPG)''' |align="left" style="background:#f0f0f0;"|''' N(UCHG)''' |align="left" style="background:#f0f0f0;"|''' N(UCHH)''' |align="left" style="background:#f0f0f0;"|''' P(MCPG)''' |align="left" style="background:#f0f0f0;"|''' P(MCHG)''' |align="left" style="background:#f0f0f0;"|''' 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 === #!/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 === === Bam to Hapinfo === * 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) === 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)=== perl ~/bin/[[hapinfo2mf-Estellar.pl]] ./ > ../Estellar2016.hapinfo2mf.txt === Hapinfo to Methylation Haplotype Load === 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=== * [[Hapinfo to MHL and MF.job]]
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