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.
R is pretty common, but if you don't know R, you could try ngsplot. It's an R script you call from the command line with various flags and config files. It can create a lot of the average gene type plots.
I ran into the same problem a while ago -- I saw a lot of fancy ChIP-seq figures with no information in the methods to describe how they were made.
So I wrote metaseq (paper, github, docs). At the same time, others wrote ngsplot and deepTools to address the same lack of tools.
ngsplot and deepTools are great for use from the command line; metaseq is more of a toolbox. Example 1 walks you through making a custom ChIP-seq figure and gives a taste for what you can do with the package.