Representing several BAM files into one?

Question

[compuTE]

Hello,

I have four samples from the same condition (BAM files) and two controls (also BAM files). I want to eventually use plotHeatmap and plotProfile from deepTools, and I dont want to have six heatmaps sitting next to each other. I want the signal of the four samples to be represented as one (they are pretty similar on the region I want to plot so I was thinking on averaging them somehow), my questions are:

1. Is bamCompare --operation mean going to average the signal of the two input BAM files? There is no complete explanation about this option in the documentation...
2. Is this the best way of doing this? It feels really weird to do this in BAM files..
3. If it is the only way, how can I do this for the four samples on the same condition? Since the software just takes two input files and the sum of the two outputs wouldnt really be the mean..

Thanks!

[puramabhi44]

Were you able to resolve this issue? I have the same problem, and any guidance would be greatly appreciated!

Thanks in advance.

[compuTE]

Hi! I didn't find a proper solution to this, other than a change of perspective about it. I think for a publication it seems more solid to show one sample to highlight the conclusion and put the rest as supplemental in case anyone wants to go check. Means are really not ideal since they are affected by outliers and could make the observation bias.

So, my advise is to just show it all, highlighting what your conclusion is from the data. Hope it helps in any way..