Question: Can I sequence Single Cell ATAC libraries with other libraries?
Answer: We do not recommend pooling Single Cell ATAC libraries with other non-ATAC 10x sequencing libraries. Sequencing ATAC libraries with other 10x sequencing libraries (SC3', SC5', CNV) in the same or different lane is not supported as the dual indexing required for ATAC libraries may cause sequencing issues for these other libraries.
Sequencing Single Cell ATAC libraries in the same lane as non-10x libraries is not supported, as we cannot guarantee that mixing libraries will not impact sequencing data quality for non-Single Cell ATAC libraries.
ATAC libraries can be sequenced with other non-10x libraries if:
- ATAC libraries are in their own lane
- i7 and i5 index read lengths are conserved: 8bp for i7 and 16bp for i5.
- R1N and R2N read lengths are at least 30bp
Refer to the following articles for more details on altering read lengths.