Visualizing bigwig tracks
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Entering edit mode
4.6 years ago
fr ▴ 210

I want to see how bigwig tracks look, but I'm not sure I'm doing things properly. When I look at them in WashU with default properties I see the following:

This shows the reads per region. The maximum of 1 in the YY axis is given because it is showing the mean of all the reads (I assume), and no smoothing is used. The Aggregate Method = Mean.

image

However, this is cumbersome and not very easy to see what is happening in those regions. A summed coverage would be more interesting. When I select instead Aggregate Method = Sum, things start to become a big clearer. I have also considered 1 pixel smoothing:

image2

Now my questions are:
- What is the "mean", "sum", etc. computed over? I cannot find the information of how many bins are being used when I right click any of the tracks.
- Prior to uploading them, I could of course bin the data myself. But then, zooming in/out, or changing locations, would always be affected by the regions I've used to define the bins. But other than this, how can I have a better control to what is being shown?

Thanks in advance

ChIP-Seq RNA-Seq • 1.5k views
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Entering edit mode
4.6 years ago
colin.kern ★ 1.1k

If it works like the UCSC browser, that is the operation that is performed at the on-screen pixel level. If your bigwig is binned in 100bp bins, let's say, but the zoom level for your browser means that each pixel is representing 500bp, then that operation will be performed over the 5 bins at each pixel to decide how to draw each of the bars.

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