Spearman correlation for ATAC data
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
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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.
Thank you very much. What is the best way to get read counts for each peak? Best
try featureCounts