Plotting ChIP seq signals in specific regions

Question

[brisbio]

I was wondering if anyone can help me. Looking on IGV at my ChIP seq data I am noticing that there seems to be an overlap between 2 different TFs binding to the same location. I know you can do read density plots to show the location across the gene where there is the highest read density. Is there a way that for all peaks where there is an overlap between the 2 TFs I can physically show that using read density? Instead of just having a number of peaks where the two overlap in genomic region.

Answer 1

[Friederike]

You can generate the density plot and heatmaps using the peaks. If you have 2 BED files with the peaks from TF 1 and those from TF 2, you can feed those into deepTools' computeMatrix as described here. (You don't need to use the scale-regions mode, in fact, I would recommend to use the reference point mode with the reference point set to the center of the peaks --referencePoint center)

[brisbio]

Thank you this is really helpful. I’ve been able to follow the documentation and done some plots. I do have another question though for each TF I have a separate bigwig file. So far I have put both TF bed files for -R and the two corresponding bigwig files for -S with a space in between. However when I plot I get two graphs one based on TF1 bigwig and the other based on TF2 bigwig. Is there a way to do it that it computes it together?

[Friederike]

Sorry, I don't get what you're envisioning. Do you have an example image you could link to?

[brisbio]

Reading that back it is quite confusing, sorry! But I managed to solve what I wanted to do, I just misunderstood part of the way computeMatrix works. However my only issue now is I have 4 replicates for each TF, therefore for each TF I have 4 bigwig files. Is there any way to merge these so I can have one plotProfile graph that merges all 4 replicates for each TF together?

[Friederike]

You may want to look into wiggletools that will allow you to generate one summarized bw file per TF, e.g. using the sum or the average (hopefully also the median).

[brisbio]

Just had a look into that and seems perfect what I want. Thank you for your help!