log2 RPKM heatmap for ATACseq

[walfr...@gmail.com]

Hi deepTools developers,

I have some ATACseq data and I want to use the computeMatrix and plotHeatmap functions to generate heatmaps.

I used RPKM normalized bigwig tracks generated by bamCoverage as input for computeMatrix. However, there are outlier peaks with high RPKM counts which dominate the heatmap. I wonder if there is anyway to plot log2 RPKM heatmaps in deepTools.

Unlike ChIPseq, there is no "input" control for ATACseq. So I can not use the bamCompare function to generate log2 fold change bigwigs.

Regards,
Walfred

[Devon Ryan]

Hi Walfred,

I think you can use wiggletools to compute the log2 of your bigWig
tracks, which you can then use instead.

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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