How do I determine how many spots are covered with tissue to determine sequencing depth needed?

Question: How do I determine how many spots are covered with tissue to determine sequencing depth needed?

Answer: Customers can estimate the % of capture area spots covered by the tissue section to determine their sequencing requirements. 

1. 1. 1. How to calculate sequencing depth on a 6.5 mm Capture Area:
         1. Sequencing = (tissue coverage area x 5,000 total spots in the capture area) x 25k read-pairs per spot
         2. Example: 50% of capture area covered by tissue section (.50 tissue coverage x 5,000 total spots) x 25k read-pairs per spot = 62.5 million paired-end reads
      2. How to calculate sequencing depth on an 11 mm Capture Area:
         1. Sequencing = (tissue coverage area x 14,000 total spots in the capture area) x 25k read-pairs per spot
         2. Example: 50% of capture area covered by tissue section (.50 tissue coverage x 14,000 total spots) x 25k read-pairs per spot = 175 million paired-end reads
   2. For an accurate number of spots covered with tissue, customers can use the Visium Manual Alignment Wizard in Loupe Browser.
   3. Many libraries will be sufficiently complex such that sequencing deeper will yield more UMI’s and genes detected. Where customers do not approach sequencing saturation at 25k read pairs per spot, further sequencing may be warranted depending on the research question.

 Products: Visium CytAssist for FFPE, Visium CytAssist for FF, Visium CytAssist for FxF