Tutorial:How to display Agilent CGH array in IGV

Question

[sacha]

CGH array output file from Agilent technology contains several lines per probe position. From line 11, each line contains all information available for one probe. The following text is an example of data for one probe. Genomics coordinate ca be found from column 8 and logRatio from column 11.

TYPE    FEATURES        DATA   
integer FeatureNum      990   
integer Row     6   
integer Col     140   
integer SubTypeMask     0   
integer ControlType     0   
text    ProbeName       A_16_P01973391   
text    SystematicName  chr8:96509647-96509706   
float   PositionX       3520.86   
float   PositionY       453.554   
float   LogRatio        -6.235932011e-002   
float   LogRatioError   6.250540449e-002   
float   PValueLogRatio  3.184428731e-001   
float   gProcessedSignal        6.201569e+002   
float   rProcessedSignal        5.372078e+002   
float   gProcessedSigError      6.279056e+001   
float   rProcessedSigError      5.449940e+001   
float   gMedianSignal   430   
float   rMedianSignal   683   
float   gBGMedianSignal 16   
float   rBGMedianSignal 46   
float   gBGPixSDev      5.600399e+000   
float   rBGPixSDev      1.890629e+001   
boolean gIsSaturated    0   
boolean rIsSaturated    0   
boolean gIsFeatNonUnifOL        0   
boolean rIsFeatNonUnifOL        0   
boolean gIsBGNonUnifOL  0   
boolean rIsBGNonUnifOL  0   
boolean gIsFeatPopnOL   0   
boolean rIsFeatPopnOL   0   
boolean gIsBGPopnOL     1   
boolean rIsBGPopnOL     1   
boolean IsManualFlag    0   
float   gBGSubSignal    405.177   
float   rBGSubSignal    626.689   
boolean gIsPosAndSignif 1   
boolean rIsPosAndSignif 1   
boolean gIsWellAboveBG  1   
boolean rIsWellAboveBG  1   
float   SpotExtentX     26.4388   
float   gBGMeanSignal   16.824   
float   47.828nSignal

You can then extract genomics coordinate and logRatio to create a bedgraph file as follow:

cat cgharray.txt | tail -n +11|cut -f8,11|grep chr|awk 'BEGIN{OFS="\t"}{gsub("-","\t",$1); gsub(":","\t",$1); print $1,$2}' > cgharray.bedgraph

Open the generated file with IGV, adjust the view with autoscale and you are done !