how to log2 y-axis score in plotProfile

[程冬]

hi, I used plotProfile to plot  profile at my enhancer summit sites. I got result like this :

but I want to log2 the y-axis score in profile plot like below figure and I couldn't find any parameter in computeMatrix and plotProfile. So, anyone know how to do this?

thanks.

my commands like this:

• bamCoverage --normalizeUsingRPKM -b ECR.treated.bam -o ECR.treated.bw
• bamCoverage --normalizeUsingRPKM -b ECR.untreated.bam -o ECR.untreated.bw
• computeMatrix reference-point -a 3000 -b 3000 -S  ECR.treated.bw ECR.untreated.bw -R  all.enhancer.summit.bed -out ECR.all.enhancer.matrix.gz
• plotProfile --perGroup --dpi 1000 --refPointLabel summit --matrixFile ECR.all.enhancer.matrix.gz --outFileName ECR.all.enhancer.matrix.pdf

[Devon Ryan]

There's no way to log2 the data once it's in plotProfile. There, you'll have to output the data (the "--outFileNameData" option) and replot it (e.g., in R).

Alternatively, you can make your bigwig files log2 (e.g., with bamCompare), then rerun computeMatrix and then plotProfile. I expect my first suggestion is quicker though.

Devon

--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51

79108 Freiburg

Germany

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