Question: What is 'read pairs per cell' and how does it relate to sequencer yield?
Answer: Flow cell yield is specific to each individual sequencer and flow cell type. The number of reads depends on the number of clusters generated. This is listed on the Illumina webpage. For example, here are the NovaSeq 6000 specifications.
For example, for the SP flow cell, Illumina specifies there should be at least 650 - 800 M reads or clusters passing filter; for the S4 flow cell, Illumina specifies there should be at least 8-10 B clusters passing filter. Illumina’s “paired-end reads” in the table above is double the number of clusters passing filter.
In the sequencing section of the User Guide, the sequencing depth required for data analysis is listed as read pairs per cell. Read pair per cell (reads per cell) correspond to the number of clusters passing filter needed for single cell analysis. One single end read = 1 cluster = 1 read pair = 2 paired end reads. The 10x Genomics Flowcell Capacity Calculator can assist in the determination of the total reads needed for a pool of single cell libraries.
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