Ns126:Heyn2016: Difference between revisions

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>Shicheng
>Shicheng
 
(36 intermediate revisions by the same user not shown)
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==Background==
==Background==
* Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer
* 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.
* WGBS by 101 bp pair-end sequencing.
* Phred Score: 33  
* Phred Score: 33  
Line 8: Line 9:


===Sample===
===Sample===
* assemble sample config file
* [[assemble sample config file]]
*ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/
*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
*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 Download===
Line 19: Line 89:


===SRA to Fastq===
===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 ===
=== 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 to Hapinfo ===
Line 30: Line 515:
  cd /oasis/tscc/scratch/ddiep/BAMfiles
  cd /oasis/tscc/scratch/ddiep/BAMfiles
  perl ~/bin/[[SaminfoPre4hapinfo.pl]] > ~/oasis/Estellar2016/SaminfoPre4hapinfo.txt
  perl ~/bin/[[SaminfoPre4hapinfo.pl]] > ~/oasis/Estellar2016/SaminfoPre4hapinfo.txt
  cd '''/home/shg047/oasis/Estellar2016/hapinfo'''
  cd /home/shg047/oasis/Estellar2016/bam
  perl ~/bin/[[bam2hapInfo2PBS.pl]] ../SaminfoPre4hapinfo.txt
  perl ~/bin/bam2hapInfo2PBS.pl ../SaminfoPre4hapinfo.txt submit nonbismark
  qsub SRX381621_tumor_breast.chr20.job
  qsub [[SRX381621_tumor_breast.chr20.job]]
* Merge hapinfo in different chrosome to one file by sample ID
* Merge hapinfo in different chrosome to one file by sample ID
  cd /home/shg047/oasis/Estellar2016/hapinfo
  cd /home/shg047/oasis/Estellar2016/hapinfo
perl [[~/bin/hapinfoMergeByChrosome.pl]]
cd /home/shg047/oasis/Estellar2016/mergeHapinfo


=== Haploinfo to Methylation Haplotype Block (MHB) ===
=== 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


=== Hapinfo to Methylation Haplotype Load ===
* 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


===trim_glore===
=== 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%]]


===Alignment===
===MHL===
* [[Hapinfo to MHL and MF.job]]

Latest revision as of 20:16, 9 January 2017

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]