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There are several causes for this which may include:
Each of these conditions could introduce more variability and increase variation of read counts to >10%.
Check that your libraries meet the minimum threshold of 6 nM or 12 nM in a 20 µL library yield for optimal performance.
Note: Quantify problematic libraries before pooling to confirm suggested molarity. Use a P10 pipette if available, and ensure pipetting equipment is maintained and calibrated.