Question: My ATAC trace looks different, is it ok to proceed?
Answer: A representative trace for an ATAC library can be found in the Chromium Single Cell ATAC Reagent Kits User Guide.
The peaks of the final trace are indicative of the periodicity of the chromatin structure and show nucleosome-free, mononucleosome, dinucleosome and multinucleosome fragments. See: What are the peaks present in my ATAC library trace?
The Multiome ATAC trace may have a high molecular weight peak at 2000bp that we have not found to significantly impact data quality. See: Why do I see an increased High Molecular Weight peak at 2000bp in the Multiome ATAC library trace?
Normal variations: Some variation in the intensity and relative sizes of nucleosome-associated peaks in the ATAC traces may be observed due to species, tissue, or sample preservation differences. Most samples have a mononucleosome peak that is similar in size or higher than the nucleosome-free peak. It is ok to proceed with sequencing such samples.
- Single peak: An elevated nucleosome-free peak often indicates reduced data quality. Traces showing only one peak should not be sequenced. See Why does my ATAC trace only have 1 peak?
- Increased mononucleosome peak: Traces showing an abnormally high mononucleosome peak may indicate an increased number of dead/dying cells or granulocyte contamination within the sample. See How do granulocytes affect my ATAC data? Exert caution when sequencing, expect an increased number of cells to be filtered out as "non-cells". Sample prep optimization is recommended.
Products: Single Cell ATAC, Single Cell Multiome ATAC + GEX