Spearman correlation for ATAC data

Question

[daffodil]

Hi, Based on the summit_abs location, I did Spearman correlation on three replicates after ATAC seq analysis; however, since I used summit_abs location, I think I have made an error. In order to generate Spearman correlations using ATAC Data, should I use a bam file or another file? Best

[ATpoint]

Please understand that people don't know your analysis and cannot see your screen. What is "however, since I used summit_abs location," what does that mean? Generally, I would do correlations on the read counts in peaks.

[daffodil]

Thank you very much. What is the best way to get read counts for each peak? Best

[gglim]

try featureCounts