Introduction to the Integrative Genomics Viewer (IGV ...Introduction to the Integrative Genomics...
Transcript of Introduction to the Integrative Genomics Viewer (IGV ...Introduction to the Integrative Genomics...
1.LaunchIGV
2.Selectreferencegenome.• ClickonHumanhg19 inthegenome
drop-downmenuintheupperleftcorner.
3. LoaddatafromtheIGVhostedserver.• SelectFile>LoadfromServer…
• OpentheTutorialsmenu(UseonMac,and+onWindows)and clickontheUIBasicscheckbox.
Fourtracksareloaded:ENCODEprojectChIP-seq datarepresentinghistonemodifications.Eachtrackisdisplayedasabarchartofsignalintensities.
IntroductiontotheIntegrativeGenomicsViewer(IGV)
Hands-onexercise:IGVUserInterfaceBasics
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MakesureyouonlyopentheTutorialsmenu.Donot checktheboxnexttoTutorials.ThatwillselecteverythingunderTutorials, butweonlywantUIBasics forthisexercise.
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ThistypeofdataisperfectforaUIbasicsexercisebecausethetracksarevisuallysimple– butthenavigationbasicsarethesamenomatterwhattypeofdatayouload.
IfthisisthefirsttimeyourunIGV,theremaybeonlyone entryinthemenu.Moreaboutthatlater...
IfyouonlyseeHumanhg18inthemenu,it’soktoselectthatinstead
4. Navigate acrossdifferentgenomiclociandatdifferentzoomlevels,fromwholegenomeviewanddowntobase-pairresolution.
4a. Startatwholegenomeview:• SelectAllfromthechromosomedrop-downmenu–OR– ClicktheHomebutton.
4b. Zoomintoviewonewholechromosome:• SelectChr1fromthechromosomedrop-downmenu–OR– Clickthe1inthegenomeruler.
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Rulerdisplaysallthechromosomes
Genomerulernowhasmoredetailsandacytoband viewofthechromosome
Atthiszoomedoutview,thegenetrackdisplaysgenedensity
Genetrackstartsshowingindividualgenes,butstilltoo
manytosee
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4c. Zoominfurther:• Clickanddragtozoominonaregionsweptoutintheruler
• Double-clickinthedatatracktozoominonapointofinterest.[Alt-clicktozoomout]
Rulermeasurementsandaredboxonthecytoband diagramshowwhereyouareinthechromosome
4d. Movearoundwithinthechromosome:• Jump toanotherregioninthesamechromosome(nochangeinzoomlevel):Clickanywherein
thecytoband diagram.
• Scroll acrossgenomecoordinates:Clickanywhereinthedatapanelanddragleft &right.
4e. Navigatetospecificlocusorgeneonanychromosome• TypeintothesearchboxintheIGVtoolbarandclickGo:
eitheralocusingenomiccoordinates(e.g.chr1:144,874-969,268) oragenename(e.g.NRAS)
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4f. Zoomintobase-pairresolution:• Keepzoominginasbefore,orclickononeoftherightmostticksonthe
“railroadtrack”zoomwidgetintheupperrightcorner.
5. Optionsforviewingthereferencesequencetrack• Clickanywhereonthesequencetoshow/hidea3-frametranslation
• Bydefault,thesequencefortheforwardstrandisshown.Clickonthearrowtoreversethestrand.
6.OptionsforviewingthegenetrackandotherannotationtracksIGVusesaUCSCbrowserstylegenerepresentation:
• Expand thetrackusingtheright-clickpopupmenu
Referencesequence
5’ UTR
Exons
Intron 3’ UTR
Featuresaredrawninasingleline,bydefault
UseSquishedforanevenmorecompactview
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