User guide

iScan System User Guide 37
Generating Normalized Data and Genotype Calls
Generating Normalized Data and Genotype Calls
ABeadChipscangeneratesintensitydata(*.idat)files.Thesefilescontainrawintensity
datavaluesforeverybeadonthescannedimage.(SeeGeneratedFilesonpage57.)
YoucanconfigureICStonormalizethedatainthesefiles.Normalizationisaprocessby
whichtherangeofintensityvaluesfor
aBeadChipstripeistransformedtomatchatarget
range.Thisresultsinfasterdownstreamprocessingtimesandoptimizedworkflow.
Normalizeddataandassociatedgenotypecallsaresavedingenotypecall(*.gtc)files.
ICSincludesanautomatedgenotypecallingfeature,calledAutoConvert,that
automaticallyconverts*.idatfilesto*.gtcfilesduring
scanning,onaper‐chipbasis,for
useindownstreamanalysissoftwaresuchasIllumina’sBeelineorGenomeStudio
Software.
ConfiguringICStonormalizeyourdatarequiresyoutosetupamappingfilethat
associatesaty peofBeadChipwithitsmanifestandclusterfiles.
1 ClicktheMenubutton intheupperleftcornerofanyICS screenandselect
Tools|Options.
2 IntheOptionsdialogbox,clicktheAutoConverttab.
Figure27ICSAutoConvertOptions
3 SelecttheEnableAutoConvertcheckbox.
4 BrowsetoanexistingmappingfileorclickNewtocreateamappingfilenow.
5 [Optional]Editthemappingfileasfollows:
a ClickEditMappingFile.
TheAutoConvertMappingdialogboxopens.
NOTE
WhenrunningunderLIMS,youcannotusetheICSAutoConvert
feature.IlluminaLIMSusesitsownbuilt‐inautomatedgenotypeca lling
feature,calledAutoCall.FormoreinformationonLIMSAutoCall,see
theIlluminaLIMSUserGuideandtheIlluminaLIMSProjectManager
Guide.