gplink操作指南.docx

gplink操作指南.docx

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gplink操作指南

IntroducinggPLINK

ThisisthescreenyouwillseeuponopeninggPLINK.

ThetoprightpaneltrackseachPLINKoperation,representingthecommandlineandtheinputandoutputfilesasatree.

ThetopleftpanelshowsthefilescontainedinthePLINKprojectfolder.

ThebottompanelshowstheLOGfilefromanyoneparticularPLINKrun.

Settingtheprojectfolders

Initiatlly,onemustsetthelocalprojectfolder.

Optionally,ifrunninggPLINKinremotemode（wherethedataandcomputationresideonaremoteserver）,wewillalsosettheremoteprojectfolderaswell.

Settingtheprojectfolders

HittheBrowsebuttontoselectalocalprojectfolder.

IfrunninggPLINKinlocalmode,thiswilltypicallybethefolderwherethegenotypeandphenotypefilesalreadyreside.

Ifrunninginremotemode,thislocalfoldercanbeanemptyfolder--itisjustusedtostoretemporaryfiles.

Herewesetthelocalprojectfolder.

Inthisexamplewearerunninginremotemode,sothisisjustanemptyfolder,wgas1.

NowweinstructgPLINKthatwearerunninginremotemode,bycheckingtheLinktoaremoteprojectboxoncewehaveselectedthelocalfolder.gPLINKusestheSSHprotocoltoconnecttoanyserverthatprovidesthisservice.Enterthehostnameandyourusernamehere.Youprobablywanttoleavetheportnumbersettothedefault,22.

Nowenteryourpasswordforyouraccountontheserver.

Nowselecttheremoteprojectfolder:

thisdialogwillappearthatlistsallthefilesandfoldersontheremotemachine.

NavigatetothefolderwhichcontainsthegenotypeandphenotypedataandthenclickOpen.

Inthiscaseweselectthefolderthatalsohappenstobecalledwgas1although,rememberthisisadifferentfolderfromthelocalone,onadifferentmachine.

Thisdialogwillappearonlyonce,atthestartofeachnewproject（althoughyoucanchangeoptionslater）.

ThetoptwooptionstellgPLINKwherethePLINKprogramresides（eitherlocallyorremotely,dependingonwhetheryouarerunninginlocalorremotemode）.

ThePLINKprefixoptionisdesigntofacilitateusingPLINKwithaclustercomputingenvironmentifitisavailable（forexample,prefacingallcommandsinbsub）.Ifyouareunfamiliarwiththeoptionand/ordonothaveaccesstoacluster,youcanignorethisoption.

Theotheroptionsonthispanelareoptional.YoucantellgPLINKtoalsouseanalternateviewer/editor（forexample,emacsorExceloranyotherprogramthatacceptsplaintextfilesasinput）byselectingtheexecutableunderUserspecifiededitor

The"autosave/updater"optioncontrolshowfrequentlygPLINKwillcheckthelocal/remotecomputer（dependingonthelocal/remotenatureoftheproject）forcompletedoperationsandregularlysavetheoperationhistory.Turningthisfeatureoffisnotrecomendedandremoteprojectswithslowconnectionsmaywishtoincreasethetimingto60secondintervals.

IfyouhavedownloadedHaploview,youcantellgPLINKwheretheHaploviewJARfileisonyourlocalmachine.ThiswillenableintegrationbetweengPLINKandHaploviewforviewingfilesanddata.

Thebottomoptionisanadvancedoptionalfeature,whichallowsyoutopassextracommandflagstoHaplovew（forexample,-memory2000tosettheamountofmemoryHaploviewhasavailable）.

AfterclickingonBrowsetospecifywhereHaploviewis（fromthepreviousgPLINKconfigurationdialog）youwillseethisdialog.NavigatetowhereHaploviewisonyoursystem

Note,typicallyyourversionofHaploviewwillbecalledjustHaploview.jar

Thisshowsthecompletedconfigurationform.

ThemostimportanttwothingsarethatgPLINKknowswherePLINK（eitherremotelyorlocally）andHaploview（alwayslocally）live.

Nexttimeyouopenthisproject,thisstepwillbeskippedandgPLINKwillrememberthesettings.

OurfirstgPLINKcommand

Nowwehavefinishedconfiguration,wearefinallyreadytostartlookingatthedata.

Inthiscase,theremoteprojectcontainsabinaryfilesetcalledexample（i.e.thePLINKdatafilesexample.bed,example.bimandexample.famalreadyexistintheremotefolder）.WecouldequallyusegPLINKwithstandardtextPEDandMAPfilesalso.

WewillusetheValidatefilsetoptionfromtheSummarystatisticsmenutoobtainbasiccountsofindividualsandSNPs（thisisequivalenttorunningPLINKwithnocommandlineoptionsotherthan–bfile

Validatefilesetdialog

Selectingthemenuoptionbringsupthisdialog.Mostdialogsforotheranalyseslooksimilartothis:

∙Inthetoppanelwespecifythedata:

eitherabinaryorstandardfileset.Hereweseetheexamplefilesetlisted.Ifotherfilesetswereintheproject,thecomboboxcouldbeusedtoselectoneofthem.Additionally,theindividualfiles（BED,BIMandFAM）canbeindividuallyspecifiedinstead（i.e.iftheydonotsharethesamefileroot,oriftheyresideinadirec