Question: Why can I not pool Multiome ATAC and Standalone ATAC libraries on certain sequencers?
Answer: Multiome ATAC libraries can be pooled with standalone ATAC libraries only on certain Illumina sequencers like MiSeq, HiSeq 2000/2500, NovaSeq 6000 (v1 reagents) sequencers which run the forward strand workflow. If pooled on a reverse complement workflow sequencer, the index primer binds to Read 1N and reads towards P5 in a standalone ATAC library. If sequenced in this manner, the indexing read will go into P5, which can lead to issues with your sequencing run and is unsupported.
Products: Single Cell Multiome ATAC + GEX