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How to increase alignment quality
Hello Developers
We used scanPav to compare genome A with B. We filtered them for more than 10 KB fragments which are present in A but absent in B. However, when we aligned the result to genome B they still show presence while there should be no match.
So, the question what is the criteria for mapping and how to get the present variation (in A genome) that is absolutely absent in the second species (B)?
Is there any criteria to increase the mapping quality?
Regards