What is the expected duplicate rate of ATAC-seq data?
Duplicate reads are usually the result of PCR duplicates during library preparation. These reads are flagged and removed during preprocessing. Since Tn5 transposase insertion is random, PCR duplicates represent artifacts that may affect downstream analysis. A low duplication rate (< 5-10%) is optimal, although a slightly higher rate is still acceptable (< 20-30%), a higher percentage may indicate issues in the sample preparation steps.
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