V[NGT[ɂ蓾ꂽf[^̉

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emailF<a href="mailto:bono@dbcls.rois.ac.jp">V_G</a>
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̈Zr[, <strong>4</strong>, e008 (2015)@<a href="http://dx.doi.org/10.7875/leading.author.4.e008">DOI: 10.7875/leading.author.4.e008</a>
Hidemasa Bono: <strong>Sequence data analysis in life science utilizing next generation sequencers.</strong>

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<h2>v </h2>
@Ȋw̌ɂĎV[NGT[ʂɎg悤ɂȂĂD܂ŁC܂܂ȉpĂĂCŋ߂ł́CQm̍ĉǂɂ鑽^̉͂Qm̐VKȉǁCgXNvg[̉ǂɂRNA]ʗʂ̑CDNA^pŇz̉́C׋ۑp̃^Qm̉͂Ȃ̂ɂȂDΉf[^͂̎@قڌł܂Ă悤ɂ݂DŁC̃r[ł́CV[NGT[ɂ蓾ꂽf[^͎̉@Cf[^x[X̃f[^͂ĂꂩЉD

<h2>͂߂</h2>
@V[NGT[inext generation sequencerFNGSjɂǂꂽz̏́Cǂ̂悤ȎsƂ^f[^ƂƂɁCSRAiSequence Read ArchivejƂ΂f[^x[Xɓo^Ă<a href="#R1"><sup>1)</sup></a>DV[NGT[ɂ蓾ꂽf[^̓o^2007N͂܂C2015N4݁CŖ3.6y^iy^1015jCf[^ʂ͖2.3y^oCgƁCێ邾łւȗʂɂȂĂi<a href="http://www.ncbi.nlm.nih.gov/Traces/sra/" target="_blank">http://www.ncbi.nlm.nih.gov/Traces/sra/</a>jĎɂ݂ƁCQm3/4߂߁C̎c̔gXNvg[CŃ^QmȂĂi<a href="#F1">}1</a>jD̃r[ł́CV[NGT[ɂ蓾ꂽf[^͎̉@D

<a name="F1"></a><div id="fig1-caption-text" style="display: none;"><strong>}1@f[^x[XSRAւ̃Gg[삲Ƃɕނ</strong>
ނ͓o^̍ۂɂgStudy Typehł͂ȂCDBCLS SRAi<a href="http://sra.dbcls.jp/search/" target="_blank">http://sra.dbcls.jp/search/</a>jɂƎɍĕނ́D
<a href="http://leading.lifesciencedb.jp/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.1.jpg" target="_blank">[Download]</a></div>[hs_figure id=1&amp;image=/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.1.png&amp;caption=fig1-caption-text]


<h2>1D}bsOƃAZu</h2>
@V[NGT[ɂ蓾ꂽf[^̉͂ɗp\tgEFȂ̓I[v\[XŖŎĝłC̃[U[eXgẽ[OXgtwitterȂǂ̃\[VfBAł̕]zĂD܂Ƃ߂SEQanswersWikiɂ́C2014N415݁C690̃\tgEFAo^Ăi<a href="http://seqanswers.com/wiki/Software" target="_blank">http://seqanswers.com/wiki/Software</a>jD̃\tgEFẤ݂CĂ邱Ǝ̂͂قړƂ̂C\tgEFA̎ގ̂͂قڏosD̂\IȂ̂ЉD玟V[NGT[Ɋ֘Azf[^̃tH[}bg܂Ƃ߂i<a href="#F4">\1</a>jD

<a name="F4"></a><div id="fig4-caption-text" style="display: none;"><strong>\1@V[NGT[Ɋ֘Azf[^̃tH[}bg</strong>
BAM`BCF`̂قׂ͂ăeLXg`łĈ܂܂ł̓t@CTCY傫Ȃ邽߁Cӂ͈kĂ邱Ƃ
<a href="http://leading.lifesciencedb.jp/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Table-1.jpg" target="_blank">[Download]</a></div>[hs_figure id=4&amp;image=/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Table-1.png&amp;caption=fig4-caption-text]

@V[NGT[璼ڂɓɂĂCSRAȂǂ̌f[^x[X_E[hɂĂCf[^͂̃nuFASTQ`̔zt@Cłi<a href="#F2">}2</a>jDFASTQt@CƂɁCf[^͂OƂăA_v^[z^OziǗsC̖ړIɂFASTQCƂ\tgEFA悭pi<a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a>jD̂̂Cf[^͂̓t@XƂȂQmɃ}bsO邩CAZu邩ɕD

<a name="F2"></a><div id="fig2-caption-text" style="display: none;"><strong>}2@f[^͂̃nuƂȂFASTQ`</strong>
FASTQ`͎V[NGT[̃[J[@ɂȂzf[^̕WIȌ`ɂȂĂD݁Cf[^x[XSRAɂĂSRA`pĂCsratoolkitfastq-dumpƂ\tgEFAɂFASTQ`ɕϊKvD́CBAM`ł̓o^邱Ƃ\zC̏ꍇbedtools̃TuR}hbamtofastqȂǂgFASTQ`ɕϊKvD
<a href="http://leading.lifesciencedb.jp/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.2.jpg" target="_blank">[Download]</a></div>[hs_figure id=2&amp;image=/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.2.png&amp;caption=fig2-caption-text]

@t@Xz񂪂łɂqgCQmz񂪂łɉǂĂ}EXCVEWEoGCȂǂ̑̌ÓTIȃfɂẮCV[NGT[ɂ蓾ꂽ[hzt@XƂȂQmzɑ΂āg\hi}bsOj邱Ƃf[^͂͂܂D̃}bsÔ߂̃\tgEFAƂẮCBowtie <a href="#R2"><sup>2)</sup></a> 邢BWA <a href="#R3"><sup>3)</sup></a> g邱ƂقƂǂłD}bsOɂ͑傫ȌvZRXgČvZԂуvD̏o͌ʂ̓Qmɑ΂BAM`̃ACgt@CƂēDBowtiȅo͌ʂBAM`̃eLXgłłSAM`ɂ蓾邪Ĉ̂̃f[^̓͂\[gꂽBMA`ł邱Ƃ̂ŁCsamtoolsƂ\tgEFApBAM`ɕϊ\[g邱Ƃ<a href="#R4"><sup>4)</sup></a>DŐVłsamtoolsiversion1.2jł͂̃\[g̕񉻂ϊ̍}ĂD
@t@XƂȂQmẑȂł̓}bsO͂łȂȂ̂ŁCV[NGT[ɂ蓾ꂽ[hźgȂ킹hiAZujKvDAZuɂ蓾̂́CBLASTȂǔzގ̌łȂ݂FASTA`̔zf[^łD

<h2>2DQm̉</h2>
@V[NGT[ƂgĂ̂́C̂̂̃Qm̉́CƂɁCqgl̃QmǂłDqgQmŜ1قǂmRNAɓ]ʂGL\݂̈̂ĉǂ̑ΏۂƂGL\[͂ł́C}bsÔ߂̃\tgEFAƂBWAg̓t[Љ邱ƂD̈ȒPɏqׂƁC}bsOɂ蓾ꂽBAMt@CCsamtoolsPicardi<a href="http://picard.sourceforge.net/" target="_blank">http://picard.sourceforge.net/</a>jgd̂郊[hzCBedtoolspăGL\݂̈̂𒊏o<a href="#R5"><sup>5)</sup></a>DāCsamtoolsɂ葽^iƂ1uCsingle nucleotide variantFSNVĵꏊ𒊏oC񓯋`uC~XZXψفCt[VtgψقƂAme[VCVCF`̃t@CƂČʂ𓾂D
@܂CGsQm͂ꍇɂ́CoCTt@Cgɂ胁`ȂVgVEVɒuDNAzǂۂɃ`~Ƃēǂ܂邱Ƃ𗘗pă`ꂽʂoWGBSiwhole genome bisulfite sequencingj@ɂ͂D`ꂽʂɉuN̂ł1uƂČo헪ƂC{Iȃf[^͂̎@̓Qm̍ĉǂ̂ƂƓłDŏIIɂ́CQmuEUƂĂ悭gIGV <a href="#R6"><sup>6)</sup></a> pāCƂȂ̈҂̖ڂŊmFD
@܂CQmVKɉǂꍇɂ̓AZu̕Kv邪Ĉ߂̃\tgEFAiAZu[j͑JĂCƂ΁Cnucleotid.esƂWebTCgi<a href="http://nucleotid.es/" target="_blank">http://nucleotid.es/</a>jɃJ^OĂDȂłCčBroad InstituteɂĊJꂽALLPATH-LG <a href="#R7"><sup>7)</sup></a> C{Platanus <a href="#R8"><sup>8)</sup></a> Ȃǂ悭gĂD͖ŗpł邪CAZû߂̃\tgEFA͈ʂɑ傫ȃKvƂȂ̂Ōl⌤̏L}Vł͓ȂƂDŁCX[p[Rs[^[iXpRj𗘗p邱ƂɂȂ邪CړIȂ獑`w̃XpRɂĂ܂܂ȃ\tgEFApł̂ŗpƂ悢D܂CL̃\tgEFAƂẮCf}[NCLC bioЂJĂCLC assembly celli<a href="http://www.clcbio.com/products/clc-assembly-cell/" target="_blank">http://www.clcbio.com/products/clc-assembly-cell/</a>j̓XpRɂȂ傫ȃKvƂMacOSXłs\ŁC܂܂ȗROɏoȂzf[^̃AZuɓKĂDAZuɂReBOꂽC̏ь낦Ă蒷z𓾂KvDĂ̂OperaƂ\tgEFAł<a href="#R9"><sup>9)</sup></a>D܂CFASTA`̃ReBÕt@CƂ𐶐̂Ɏg[hzFASTQ`̃t@CC}bsOɎg\tgEFAiBWA邢BowtiejɂĎsCmap`̌ʃt@C𓾂D̂̂COperaNFASTA`̔zt@C𓾂邱ƂɂC菭ȂCCϓIɂ蒷ȂReBOD炦QmźC߉cDNAA~m_zɑ΂zގɂAme[VCŏIIɂGTF`iGFF`j̃t@C𓾂D

<h2>3DgXNvg[̉</h2>
@}CNACpnCu_C[[V@x[Xɂ@嗬łRNA]ʗʂ̑CV[NGT[pRNA-seq@Ƃđ낤ƂĂD́C]ʂꂽRNA̔zׂĉǂCꂼ̌ꂪR]ʒPʁi`qj̔xƂ@łDāCBodymap@Ƃ΂@ł́CESTiexpressed sequence tagjƂ΂mRNA̔zfЂNX^OC]ʒPʂƂɂ̐𐔂邱Ƃɂ`qʂ͂Ă<a href="#R10"><sup>10)</sup></a>DRNA-seq@́C܂ɎV[NGT[gƂɂ肱Bodymap@ȂƂ̂łDRNA-seq@ɂ蓾RNA]ʗʂ̒PʂƂāCRPKMireads per kilobase per million mapped readsj悭pD͐Kꂽ`qʂŁC100̃[hz}bsO]ʎY̒1000ƂƂ̃}bsOꂽ[hz̐ł<a href="#R11"><sup>11)</sup></a>D܂CRPKM̑Ɏg邱Ƃ̑FPKMifragments per kilobase of exon per million mappedjقړŁCfЂƂ̐Kꂽ`qʂłDRNA-seq@ɊւĂCt@XƂȂQmɃ}bsO邩AZu邩ɕD
@}bsOɂ@ł́CGL\[͂ƓBowtieBWAƂ}bsÔ߂̃\tgEFAgDCRNAɓL̃XvCVOɑ΂ACgKvɂȂDŝTopHatƂ\tgEFAŁCTopHatBowtieN邽߁CRNA-seq@ł̓}bsOBowtieg邱Ƃ<a href="#R12"><sup>12)</sup></a>D̂̂CQm̂ǂ̈ʒuɈ`q邩ȂǂLqQmAme[Ṽt@CȉꍇCGTF`jgCCufflinksƂ\tgEFAɂIIXvCVOɂXvCXoAgXgAbv<a href="#R13"><sup>13)</sup></a>DCufflinksɂo͂`qʂFPKMłDCufflinks͕̃\tgEFAȂC̌vZXebvKvł͂邪CCuffdiffɂw肵2̏Ԃ̈`qʂ̍𓯒肷邱ƂłDɁCCufflinkšʂǂݍR/Bioconductorɂĕ֗Ɏg悤ɂcummeRbundƂpbP[WDgXNvg[͂̂߂̑̃\tgEFAR/BioconductorŊJĂ邱ƂCȂf[^͂i߂₷֗ł<a href="#R14"><sup>14)</sup></a>DCTopHatiBowtiejŝCufflinkssƂẢߒ͕Kvȃ̗ʂCCPUڂĂ}VłĂ1CPUŎs镔ȂǁCvZɂ͐Ԃ̃I[_[DŁC荂ȃ\tgEFÅJi߂Cŋ߂ł́CACgk-merJEg邱Ƃɂ`qʂ@ڂĂD̑\Iȃ\tgEFASailfish<a href="#R15"><sup>15)</sup></a>D̃\tgEFA̓gXNvg[młȂƗpłȂCǃCfbNX쐬Ă΁CƂFASTQt@CƂɂȂ荂Ɉ`qʂłD
@AZuɂ@ł́CTrinityƂ\tgEFA悭g<a href="#R16"><sup>16)</sup></a>DKvȃ̗ʂvZԂ̂_ł邪C`w̃XpRłpłD
@܂ł̎菇ɂ`qPʂŔʂʂĂ܂΁C}CNAC͂ł̎菇قڂ̂܂ܗpłDo`qZbg`qŜ݂Ăǂ݂̂̂ɂ悭p̂GSEAigene set enrichment analysisj@ł<a href="#R17"><sup>17)</sup></a>DCGL\[͂̂ɏqׂChIP-seq@ȂǂɂĂGSEA@͗LłDȂłCDAVIDƂ΂EFuc[̓C^[tF[X悭łĂ֗ł<a href="#R18"><sup>18)</sup></a>DOMIMCGene OntologyCPathwayƂ@\ւ̈`qAme[V𗘗pf[^̉߂́C}CNACɂf[^͂ƓlɁCV[NGT[ɂ蓾ꂽʂ̃f[^߂iƂėLłi<a href="#F3">}3</a>jDɍŋ߁C_f[^x[XłPubMedɂĂ̘̂̂_ɕt^ĂMeSHimedical subject headingsjgGSEA@ɂ͂@R/Bioconductor̃pbP[WmeshrJCf[^͂̃oG[VɍL<a href="#R19"><sup>19)</sup></a>D

<a name="F3"></a><div id="fig3-caption-text" style="display: none;"><strong>}3@DAVIDɂGSEA@̗̉͂</strong>
`q̃t@Xf[^ZbgłRefExi<a href="http://refex.dbcls.jp/" target="_blank">http://refex.dbcls.jp/</a>jɂCgDɓٓIȔp^[`qDAVIDɂGSEA@̗̉͂D̑ɓٓIɔ`q̓Gene OntologyBiological Process̃Ame[Vg͂D̑̋@\ƂĒmӂȂǂ̓`qxŒoĂD
<a href="http://leading.lifesciencedb.jp/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.3.jpg" target="_blank">[Download]</a></div>[hs_figure id=3&amp;image=/wordpress/wp-content/uploads/2015/05/Bono-4.e008-Fig.3.png&amp;caption=fig3-caption-text]


<h2>4DDNA^pŇz̉</h2>
@ȑOCDNA^pŇDNAz͂@ƂăN}`Ɖu~ichromatin immunoprecipitationFChIPj@C2000NO2000N㒆ɂẮCDNA̔zfЂ}CNACɂ茟oChIP-on-chip@pĂDāC}CNAC̑ɎV[NGT[pDNA̔zfЂǂ@JChIP-seq@Ƃ΂悤ɂȂ<a href="#R20"><sup>20)</sup></a>DChIP-seq@ł́CDNA^pNFR̂pĂꂪDNA̔zfЂ͂D^[QbgƂȂ^pNƂăqXgƓ]ʈqDƂɌDNAzǂ邱ƂɂQm̂ǂ̗̈ɌĂm邱ƂłCQm̂ǂ̈ʒuɈ`q邩ƂQmAme[VƂ킹邱Ƃɂ蒼ړIȓ]ʐ̊֌WłD
@ChIP-seq@ɂẮCN}`Ɖu~@ɂDNA^pNɌDNA̔zfЂt@XƂȂQmɃ}bsOCꂽBAM`̃ACgt@C͂ƂāCMACSƂ\tgEFAgʂ𐄒肷<a href="#R21"><sup>21)</sup></a>D錋ʂ́CF̂̔ԍC̏ꏊistartendjƂ̏ꏊł̃s[N̒lꂽBED`̃t@CłD̏񂩂Qm̂ǂɃs[N邩킩D̃QmɂʒuǂCQmAme[VƂR/BioconductorȂǂg͂DChIP-seq@ɂf[^͂ɂނ̂́CghƂ邩ǂ臒l̐ŁC΂͎ۂ̃f[^݂ČXɌ߂ĂKvD܂Cꂽz̓i]ʈq̏ꍇɂ́C]ʈqz񃂃`[tjm肽ꍇɂ́C̔z𒊏oACĝC̔z̓WebLogopĕpo鉖傫\悤Ȃǂ̎i<a href="#R22"><sup>22)</sup></a>D

<h2>5D^Qm̉</h2>
@V[NGT[ɂ׋ۑp̑ŜDNA̔zǂɉǂł悤ɂȂCVbgK@ɂ׋ۑp̑SQm͂@C16S rRNÂ݂ǂ׋ۑpɑ݂e̍׋ۂ̊͂@JĂĎʁCqg׋ۑp̃^QḿCqgC}EXɂŌf[^x[XSRAɑo^ĂD16S rRNA͂@́Cǂꂽ[hzɊ܂܂16S rRNA̔z񂪃f[^x[Xꂽm16S rRNA̔ẑǂɃ}b`邩T̂łDSQm̉͂ɂẮCɂSQmz̉ǂƓXebvӂށD܂Cǂꂽ[hzm̃f[^x[Xɂ邱ƂȂAZuD̔z񂩂^pN̔zR[hORFoCꂽA~m_zzƂāC܂łɒmĂA~m_z̃f[^x[Xɑ΂BLASTȂǂgzގĎʂCzގɂƂÂ@\Ame[VCŏIIɁCKEGGCOGƂނ̂߂̃f[^x[Xpċ@\ނD

<h2>6Df[^̍ėp</h2>
@V[NGT[ɂ蓾ꂽf[^͊{Iɂ͌f[^x[XłSRAɓo^D́C͌ʂ̍Č̒Sۂ̂߁CāCȊw̐iŴ߂łC݁CꂪvȂ悤Ȏgꂻ唭邩ȂłDȂCėwFANTOMvWFNgɂč쐻ꂽESTf[^x[X́CiPSזE̕U4̈qi荞ނƂɎgꂽi<a href="http://www.osc.riken.jp/contents/fantom/" target="_blank">http://www.osc.riken.jp/contents/fantom/</a>jD悤ȂƂN悤CV[NGT[ɂ蓾ꂽf[^͌f[^x[X֓o^ĂׂȂ̂łD킪DDBJiDNA Data Bank of Japanj͕čNCBI≢BEBIƃf[^Ă̂ŁCDDBJDRAiDDBJ Sequence Read Archivejɓo^ĂSRAɓo^̂ƓłCeʂ̃f[^̓]X[Yɓo^iށD
@܂Cqgl肷\̂`wIȃf[^ѕ\^̏ɊւẮCDDBJJGAiJapanese Genotype-phenotype Archivejɓo^Dɂ́CȊwZpU@\oCITCGXf[^x[XZ^[iNational Bioscience Database CenterFNBDCjɂĔFꂽp|V[ꂽf[^݂̂o^łDNBDCł̓qgɊւ邳܂܂ȃf[^L邽߂̃vbgtH[gNBDCqgf[^x[Xh^pĂi<a href="http://humandbs.biosciencedbc.jp/" target="_blank">http://humandbs.biosciencedbc.jp/</a>jCV[NGT[ɂ蓾ꂽf[^ɊւĂJGAɓo^邵݂ɂȂĂD
@_ł̓f[^~ςقɏd_Ă悤ɎvȂCCf[^x[Xɒ~ςꂽf[^ėpĂɈႢȂ<a href="#R23"><sup>23)</sup></a>D̂߁CׂpɔāCǂC̃f[^𔭕\_͂ǂꂩȂǁCzf[^̂̂łȂCɊւf[^i^f[^jƓo^̉Ȋw̔Wɍvł悤SĂقD

<h2></h2>
@f[^x[XSRAɂ́CłɁgXhV[NGT[瓾ꂽf[^o^ĂDȂCł̓V[NGT[̎ނςĂf[^͂̎菇傫ς邱Ƃ͍lȂDȂ킿Cf[^͂̎@ƂĂ͂xł܂ĂD́CC^[tF[X̉ǂȂǂɂf[^͂ɂn[hw͂ȂCwҎgV[NGT[ɂ蓾ꂽf[^͂鎞ɂȂĂƂ낤D

<h2> </h2>
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</ol>
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<span class="author">V_ GiHidemasa Bonoj</span>
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