Heatmap plotting and interpretation

[Krithika-Bhuvan]

Hello, I am a new user of the deeptools package. I have a question related to the Heatmap plotting and interpretation. I have bulk ATAC seq data for a celline with various conditions. Primary analysis was done from which peaks were obtained in the form of bed files. I also have H3Kac bed and bigwig file for the parental cell line.

Question - I would like to know what is the best way to plot the heatmap to answer question "whether the condition causes chromatin to close or not".

• It would be great to get some feedback based on your experience on what inputs to use as as the "-S" parameter and "-R" parameter, and what the heatmap should look like in order to answer the question of interest.
• So far I converted the sample bed -> bam -> bigwig file. I input the bigwig file as the "-S" parameter. Is this correct ? Or should i input the sample data as a "-R " file ?
• I have tried using H3Kac sample as the "-R" file - would this help in answering the question of interest ? Thank you

[WardDeb]

Hi,

You should first obtain a set of differentially accessible regions depending on your conditions. Deeptools is not suited for this, but you can have a look at snakePipes, AOS, or something like diffBind. There are quite a lot of options out there.

Once you have a set of regions in bed format, you can use plot the ATAC/ChIP signal on those by using computeMatrix and plotHeatmap. You are correct that the sample signal (in bw format) should be inputted under -S, the differential regions in bed format go via -R.

Feel free to re-open if you need more information or something is unclear.

Ward