**320**wrote:

In a number of ChIPseq papers I have seen graphs that have on the y-axis plotted "peak frequency" and on the x-axis plotted "log 10 (distance to transcription start site)"

I have also seen common ChIPseq plots showing on the y-axis "reads per million mapped reads" and on the x-axis "Distance to transcription start site."

However, none of these papers mentioned what software was used to generate said plots, and I was wondering if anybody here might know this information?

It would also be beneficial if anyone had a recommendation as to what kinds of plots they frequently encounter in day to day ChIPseq papers that they consider to be *almost necessary* to include in any ChIPseq paper.

Can you provide some specific references? Your description mentions simply x,y plots, which can be drawn with virtually every graphing program ever written. Is your question more about graphing programs? Or more about software for pushing around ChIP Seq data?

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