Question: Can I sequence Multiome libraries on the Nextseq 1000/2000?
Answer: We have tested Multiome libraries on the NextSeq 1000/2000 instrument. Please find a summary of the sequencing metrics & base composition in this Technical Note.
For Multiome ATAC libraries sequenced on NextSeq1000/2000, the FASTQ files generated by the instrument are incompatible with Cell Ranger ARC 1.0.x. In this case, customers should start from the BCL files, and run either cellranger-arc mkfastq or Illumina's bcl2fastq to obtain the FASTQ files. Once that's done, the FASTQ files should be compatible with Cell Ranger ARC. Our latest version 2.0 of Cell Ranger ARC will support the FASTQ files generated onboard by these sequencers.
For Multiome GEX libraries sequenced on NextSeq1000/2000, please do make sure indexes have sufficient diversity in the index read. We have more information in this article: Is nucleotide diversity in the index read important for Illumina sequencing?
Note that the Nextseq 1000/2000 systems do not require a custom recipe for sequencing.
Products: Single Cell Multiome ATAC + GEX