Question: Why might my molecule size be less than what I expected for my Genome library (Supernova or Long Ranger)?
Answer: The high-molecular weight DNA is denatured prior to running the Chromium chip. Therefore single-stranded, enzymatic-induced nicks (or other single stranded damage, such as due to heat) may result in shorter molecule lengths being incorporated into GEMs. Unfortunately, there is no way to assess nicking prior to running the 10x workflow and seeing the result. Here is a Tech Note with more information and guidance on how to reduce single-stranded nicking.