There is one more thing to say about the HITS project. Using bowtie worked well enough that I feel comfortable posting a plot similar to Fig 2 of the paper. Each point represents one of 1148 genes plotted. The x-axis is saturation (fraction of TA sites in that gene which were hit by the transposon in the library) and the y-axis is the selection index (ratio of total HITS in the lung compared to the library).
It doesn't look exactly like the paper, but it's pretty good.
I couldn't get matplotlib to do the semi-log plot, so I used R:
And that really is it for this. Here is hemR again: