An Introduction to the ISB-CGC Web App IGV - GitHub · brought to you by The ISB Cancer Genomics...
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An Introduction to the ISB-CGC Web App IGV
Transcript of An Introduction to the ISB-CGC Web App IGV - GitHub · brought to you by The ISB Cancer Genomics...
broughttoyouby
TheISBCancerGenomicsCloud
AnIntroductiontotheISB-CGCWebAppIGV
https://isb-cgc.appspot.com
MainLandingPage• Handyplacetoaccessdocumentation,code,andsendfeedback• Youmayonly loginusingaGoogleManaged identitybyclickingthesignin button
1. Logintothesystem2. CreateacohortofonlyCCLESamples
3.ClickViewFilesButton
4.FileListingPage• Youcanseewhatkindoffilesareavailableforthecohortyouarelookingatbasedonsamplebarcode.• Youcanalsodownload thefilelistasaCSV.Note:thatifthelistoffilesistoolarge,youwillgetanerror.Trymakingthecohortsmallertotrimdownthefilelistsize.
• IfthefileisavailableinGoogleGenomics, thentheIGVcolumnwillbepopulatedwithaGA4GHcheckbox.• IfthefileisavailableinGoogleCloudStorageasa.bamfile,thentheIGVcolumnwillalsohavethatoption available.• Thecheckboxeswillbedisabled ifyoudonothavethecorrectpermissions toviewthedata.• SelectingoneormorewillactivatetheLaunchIGVbutton.
4.FileListingPage
5.IGVBrowser
• Youwillbeprompted tologinagaintoauthorizeaccessoftheinformationrequired todisplay.Pleasebesuretoallowpop-upsonthispageforthat,otherwiseyoumayreceiveanaccessdeniederror.
• Here,wehavethetwosamplesthatwerepreviously selecteddisplayedandtheIGVbrowserisaccessingthereadsfromGoogleGenomicsusingtheGA4GHAPI.
6.AllTCGACohort
7.AllTCGACohortFileListing• Selectedareallfilesthatwereproducedusing theIlluminaHiSeq
• NotethattheentireIGVcolumnhasCloudStoragedataavailable.However,thecheckboxesaredisabledbecausethisuserhasnotauthenticatedandauthorized theirERACommons ID.
• Afterauthenticating, thesecheckboxeswillbeactive.
8.AssociatingyourGoogleIdentitywithavalidNIHlogin.
• Documentationcanbefoundhere:• ShortVersion:http://bit.ly/1TJErfN
• LongVersion:http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/webapp/Gaining-Access-To-TCGA-Contolled-Access-Data.html
• Note:ToaccessTCGAcontrolled-accessdata,youmustalsobeauthorizedbydbGaP.
9.IGVBrowser• Youwillbeprompted tologinagaintoauthorizeaccessoftheinformation requiredtodisplay.Pleasebesuretoallowpop-upson thispageforthat,otherwiseyoumayreceiveanaccessdeniederror.
• Here,wehavetwosamplesandwearelooking at.ThelabelsonthetwotracksshowthattheyareTCGAsamplesandGCSbamfiles.
• Note:thisisamockbamfilethathasbeenassociatedwitharealTCGAsampleidentifier.
Acknowledgements
ThecopyrighttotheIntegrativeGenomicsViewerisheldbytheBroadInstitute,andthesoftwarehasbeenreleasedundertheMITLicense.FormoreinformationaboutIGVpleaseseetheIGVHomePage ortheIGVGithub Repository.
WearegratefultotheIGVteamfortheirassistanceinintegratingtheIGVintotheISB-CGCwebapplication.
