Entering edit mode
11 hours ago
alevbozan18
•
0
I am trying to use Checkm to assess contamination and completion levels of some SAGs. The results produced from Checkm by using a custom HMM marker file is completely different from the ones that were calculated at the sequencing center. My advisor who previously used the same data says she validated the values before so they should be the same. What can I do to solve this problem?
Impossible to answer with the little information you provided. It's like saying that your soufflé didn't rise, and we are supposed to guess which one out of many reasons is the culprit.
It could be as simple as you doing something wrong. Or the program versions are different between your and the sequencing center. Or you are not using the same set of HMM markers. Or the SAG files got mixed up.
I think your adviser should either guide you better, or maybe they can replicate the results given the previous experience. How can strangers on the internet who are given scarce information do a better job than a living person who has already done this?