Question: Plotting multiple signal files against a single genomic region
gravatar for keller.mckowen
4 days ago by
keller.mckowen10 wrote:

I would like to create a sorted heatmap around a single gene region, across over 1600 experimental samples. In each experiment, a TF has been knocked down in a cell line. I have processed the data and normalized the samples against a negative control for each replicate plate. I now have normalized bigwig files.

I would like to make a heatmap in which each signal line comes from a different bigwig file in my sample library. The region would be the same for every line, my gene of interest. Using this, I could sort the experiments by which had a strong effect on my gene.

This seems like a useful function to add to an analysis suite such as Deeptools. I will try to implement a solution myself. But I am certain someone here can come up with a more elegant and integrated solution that I could.

Thank You for your consideration. -Keller

rna-seq chip-seq deeptools • 48 views
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