10x Genomics Support/Single Cell ATAC/Documentation/Sequencing/

Sequencing Requirements for Single Cell ATAC

The Chromium Single Cell ATAC Solution produces Illumina® sequencer-ready libraries.

Single Cell ATAC Libraries (v1, v1.1, and v2 Chemistries)

Sequencing requirements of Multiome ATAC libraries require different considerations, refer to the Sequencing Requirements for Single Cell Multiome ATAC + Gene Expression page for specifications.

Supported Sequencers:*

  • Illumina® NovaSeq 6000
  • Illumina® HiSeq 3000/4000
  • Illumina® HiSeq 2500
  • Illumina® NextSeq 500/550
  • Illumina® NextSeq 1000/2000
  • Illumina® MiSeq

Recommended Sequencing Depth: 25,000 read pairs per nucleus (50,000 individual reads. 25,000 from R1, 25,000 from R2)

Dual-Indexed Sequencing Run: Single Cell ATAC libraries are dual-indexed.

PhiX Spike-In Recommendations: 1%.

ReadRead 1i7 Indexi5 IndexRead 2
PurposeTransposed DNASample Index10x BarcodeTransposed DNA
Length5081650 **

* Do not pool Chromium Single Cell ATAC libraries with other 10x libraries while sequencing

** Can be 1 bp shorter to accommodate NovaSeq v1.0 100 cycle kits

Document Type

Last Modified
August 2, 2023