Tutorial: How to display Agilent CGH array in IGV

1

sacha •

**2.0k**wrote:CGH array output file from Agilent technology contains several lines per probe position.
From line 11, each line contains all information avaible 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 !