Question: How do I determine the average fragment size of a Single Cell ATAC or Multiome ATAC final library?
Answer: Select the region between 175-1000bp to determine the average fragment size of a Single Cell ATAC library. Lower molecular weight (≤ 150 bp) and/or a high molecular weight (~2,000 bp) product may be present. These do not affect sequencing and should not be included when determining average fragment size.
Note: In Multiome ATAC final libraries, you may notice an increase in the high molecular weight peak at 2000 bp compared to what we normally see in standalone ATAC assays. This is normal and does not significantly impact assay performance (Why do I see an increased High Molecular Weight peak at 2000bp in the Multiome ATAC library trace?).
Example representative BioAnalyzer trace with the 175-1000bp region selected:
Products: Single Cell ATAC, Single Cell Multiome ATAC + GEX