introduction to the integrative genomics viewer (igv ...introduction to the integrative genomics...
TRANSCRIPT
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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