When analyzing ATAC-seq data, I merged the final.bam files of two replicates from the same sample and then used the merged BAM file to call peaks. However, I found that for one sample group, the number of peaks increased dramatically from ~26,129 and ~23,829 (in individual replicates) to ~107,070 (after merging). How should I handle and analyze this issue?
I'm considering adjusting the -q parameter (FDR cutoff) in MACS2 to 0.01, but this would also reduce the number of peaks in my other samples. Are there alternative solutions?
When analyzing ATAC-seq data, I merged the final.bam files of two replicates from the same sample and then used the merged BAM file to call peaks. However, I found that for one sample group, the number of peaks increased dramatically from ~26,129 and ~23,829 (in individual replicates) to ~107,070 (after merging). How should I handle and analyze this issue?
I'm considering adjusting the -q parameter (FDR cutoff) in MACS2 to 0.01, but this would also reduce the number of peaks in my other samples. Are there alternative solutions?