Question: We have been using an Illumina NextSeq 500 to sequence our libraries, but we would like to resequence some of our old libraries on NovaSeq to improve sequencing saturation. Is it possible to combine the old NextSeq BCL files with the new BCL files from NovaSeq?
Answer: You wouldn't directly combine the BCL files, but instead you would demultiplex your data from the different sequencing runs separately using
mkfastq, then combine the FASTQ data by providing multiple comma-separated values (i.e. paths to the directories containing the FASTQ files) to the
--fastqs option of
This page details how to do this for
cellranger count (the same would apply to other 10x pipelines).