1. What is Illumina Calculated Signal Intensity?

Definition: This calculator computes the average signal intensity in Illumina sequencing by dividing the sum of pixel values by the number of clusters.

Purpose: It helps researchers and bioinformaticians quantify the average signal strength per cluster in sequencing data.

2. How Does the Calculator Work?

The calculator uses the formula:

Where:

• Intensity — Average signal strength (unitless)
• Sum Pixel Values — Total pixel values across all clusters (unitless)
• Number Clusters — Count of sequencing clusters (number)

Explanation: The formula calculates the mean signal intensity per cluster, which is important for quality assessment in sequencing runs.

3. Importance of Signal Intensity Calculation

Details: Signal intensity measurements are crucial for assessing sequencing quality, identifying potential issues, and ensuring data reliability.

4. Using the Calculator

Tips: Enter the sum of pixel values (from sequencing data) and the number of clusters. Both values must be positive numbers.

5. Frequently Asked Questions (FAQ)

Q1: What is a typical intensity range in Illumina sequencing?
A: Typical values range from 1000 to 5000, but this varies by instrument and chemistry.

Q2: How do I obtain the sum pixel values?
A: This is usually provided in the sequencing output files or can be calculated from image analysis.

Q3: What does low intensity indicate?
A: Low intensity may suggest poor cluster generation, reagent issues, or focus problems.

Q4: Can I use this for different sequencing platforms?
A: The calculation is specific to Illumina's imaging system, though similar principles may apply.

Q5: How does intensity relate to base calling?
A: Higher intensities generally correlate with better base calling accuracy.