Sequencing Requirements for Single Cell ATAC

Specifications, Last Modified on May 18, 2021, Permalink

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

Single Cell ATAC Libraries (v1 and v1.1 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:*

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. Please note, this is different than most 10x products which are single-indexed.

PhiX Spike-In Recommendations: 1%.

Read Read 1 i7 Index i5 Index Read 2
Purpose Transposed DNA Sample Index 10x Barcode Transposed DNA
Length 50 8 16 50 **

* 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