Question: What are the minimum recommended sequencing specifications for Visium libraries?
Answer: The recommended sequencing depth for the Visium library depends on several factors (tissue complexity, tissue coverage, experimental goals) and can be calculated as per the example below.
We recommend a minimum of 50k read pairs per spot covered with tissue.
Estimate the % of capture area covered by the tissue section based upon the H&E brightfield image.
(% tissue coverage area * 5000 total spots in the capture area) * 50,000 reads pairs per spot
Example: 50% of capture area covered by tissue section
(.50 tissue coverage * 5000 total spots) * 50,000 read pairs per spot
= 125 million read pairs (250M total reads)