It’s important to test the quality of your samples before submitting them for sequencing. Our policy is to charge for failed runs if the problem is sample-specific (we run a control on each flow cell to verify that our instrument and reagents worked properly).
We recommend three quality control steps:
Determine sample concentration: We recommend using a fluorescent nucleic acid detection method such as the Qubit since this is more specific than absorbance methods. The Qubit will not over-estimate sample concentration in the presence of unincorporated nucleotides like a spectrophotometer can.
Determine sample size: The Agilent Bioanalyzer generates an electropherogram showing the size distribution of each sample. Researchers may be trained to run Bioanalyzer assays for themselves, or may drop off samples for the staff to run.
- Use QPCR to determine sample concentration: This is the most accurate sample quantification method since only adapter-ligated inserts will be counted. Illumina offers a protocol for pre-sequencing QPCR, or you may use a commercially available kit. Researchers may self-run the QPCR assay after training on our QPCR instruments, or may request that the staff perform QPCR as a service. When we perform QPCR as a service, we guarantee to deliver at least 2/3 of Illumina's advertised optimal number of reads per lane/run. To request QPCR service, please email us.