How many reads do I need for E. coli Spike-in DNA and the K-MetStat Panel?

In general, ~1% of total sequencing reads should be assigned to spike-in controls. This sequencing bandwidth provides many thousands of spike-in reads, which is adequate to examine SNAP-CUTANA™ Spike-in recovery and/or to use E. coli reads for normalization. It also prevents spike-in reads from swamping sequencing data, ensuring that sufficient reads (3-8 million) are aligned to the species reference genome for biological analysis.

Note that the spike-in sequencing bandwidth may be higher or lower depending on target abundance, sequencing depth, and other factors. For instance, the IgG negative control often has 10-20% of reads assigned to the K-MetStat Panel, while a high abundance target (e.g. H3K27me3) may have 0.1-1%. Outside of this range, consider adjusting the spike-in dilution to be optimal for future experiments.