Dear colleagues,
A questions popped up while examining the RNA-seq material.
When examining Per Base Sequence Content of FastQC the Babraham institute describes the following thresholds:
Warning This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. Failure This module will fail if the difference between A and T, or G and C is greater than 20% in any position.
Could someone explain why the differences are calculated only between A and T as well as G and C?