Question: Plotting ChIP seq signals in specific regions
0
gravatar for emilyprice16
5 weeks ago by
emilyprice1620
emilyprice1620 wrote:

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.

chip-seq • 177 views
ADD COMMENTlink written 5 weeks ago by emilyprice1620
1
gravatar for Friederike
5 weeks ago by
Friederike6.5k
United States
Friederike6.5k wrote:

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)

ADD COMMENTlink written 5 weeks ago by Friederike6.5k

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?

ADD REPLYlink written 5 weeks ago by emilyprice1620

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

ADD REPLYlink written 5 weeks ago by Friederike6.5k

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?

ADD REPLYlink written 4 weeks ago by emilyprice1620

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).

ADD REPLYlink written 4 weeks ago by Friederike6.5k

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

ADD REPLYlink written 4 weeks ago by emilyprice1620
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