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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