Differences in DeepTools Heatmap Resolution Driven by Bed File

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 this:

>     computeMatrix reference-point \
>     -S /home/ec2-user/atac_analysis_gorkin/heatmaps/I315I-R1_final.bw \
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/I315I-R2_final.bw \
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/I315R-R1_final.bw \
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/I315R-R2_final.bw \
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/I315X-R1_final.bw \
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/I315X-R2_final.bw \
>       -R /home/ec2-user/atac_analysis_gorkin/heatmaps/gain_WTvW281X.bed
>        /home/ec2-user/atac_analysis_gorkin/heatmaps/loss_WTvW281X.bed \
>     --referencePoint center \
>      -a 2500 -b 2500 --outFileName /home/ec2-user/atac_analysis_gorkin/heatmaps/matrix_compute_I315X_test.tab.gz
>     
>     plotHeatmap \
>      -m /home/ec2-user/atac_analysis_gorkin/heatmaps/matrix_compute_I315X.tab.gz  \
>      -out /home/ec2-user/atac_analysis_gorkin/heatmaps/I315_heatmaps_I315IvI315X \
>      --heatmapHeight 15  \
>      --zMax 15 \
>      --missingDataColor 1 \

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.

Has anyone encountered something like this before? 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.

Heatmap with high resolution:
BED file used here (31,568 lines):
chr2 53505719 53506219
chr5 95712381 95712881
chr7 22786177 22786677
chr6 163745824 163746324
chr3 46114243 46114743
chr16 77298533 77299033
chr6 154555094 154555594
chr7 7099406 7099906
chr14 35607752 35608252
chr3 141084100 141084600
…

Heatmap with low resolution
BED file used here (36451 lines):
chr3 23981877 23982377
chr19 27716797 27717297
chr8 6503164 6503664
chr9 96499044 96499544
chr5 103923705 103924205
chr17 39177255 39177755
chr3 170438004 170438504
chr19 27995789 27996289
chr12 65525854 65526354
chr6 129369187 129369687
chr19 53892424 53893417
chr15 77859264 77859764
…

Any suggestion on how to correct this and make it consistent between the two different regions.