Differences in DeepTools Heatmap Resolution Driven by Bed File

[garrettc00per]

deeptools 3.5.4 Python 3.10.13

Hi! I'm using DeepTools to plot coverage over a list of significantly differential accessible peaks from ATAC-seq data. However, I'm running into a strange issue: the resolution of the heatmap seems to vary depending on which BED file I use, even though the underlying BigWig files and sequence data are exactly the same. Here is my code I am using to plot both of these graphs, the only thing different is the inputted bed files:

computeMatrix reference-point
-S /home/ec2-user/atac_analysis_gorkin/heatmaps/1-R1_final.bw
/home/ec2-user/atac_analysis_gorkin/heatmaps/1-R2_final.bw
/home/ec2-user/atac_analysis_gorkin/heatmaps/2-R1_final.bw
/home/ec2-user/atac_analysis_gorkin/heatmaps/2-R2_final.bw
/home/ec2-user/atac_analysis_gorkin/heatmaps/3-R1_final.bw
/home/ec2-user/atac_analysis_gorkin/heatmaps/3-R2_final.bw
-R /home/ec2-user/atac_analysis_gorkin/heatmaps/loss.bed /home/ec2-user/atac_analysis_gorkin/heatmaps/gain.bed \ --referencePoint center
-a 2500 -b 2500 --outFileName /home/ec2-user/atac_analysis_gorkin/heatmaps/matrix_compute_loss_only.tab.gz

plotHeatmap
-m /home/ec2-user/atac_analysis_gorkin/heatmaps/matrix_compute_loss_only.tab.gz
-out /home/ec2-user/atac_analysis_gorkin/heatmaps/heatmaps_loss_only
--heatmapHeight 15
--zMax 10
--missingDataColor 1 \

The command runs fine and a plot is outputted. Both BED files seem properly formatted and I don’t see any glaring differences between them. However, the resulting heatmap from the second BED file looks much more pixelated and of lower resolution. Further I have plotted on the overlap between the two bed files and I am still getting the pixellated heatmap, so this is not that the regions are different.

Any suggestions on how I can make the resolution more consistent across different BED files? The current difference makes it challenging to publish the figures since they look so different.