Hello everyone! I am new to the channel, so excuse me if this question has been answered in the past. I have noticed a difference in the calculation between Eager1 and Eager2 in the way it calculates the Cluster Factor when DeDup is used. In Eager1, I have understood that it gets caclulated by mapped reads / mapped reads after RMDup, but in Eager2, if we do the same, the result is not the same as the reported one. Could you please explain how it is calculated in Eager2?

Καλησπέρα Charoula! You can check the specific explanation of that, and any other, column of the MQC stats table in the eager output documentation: https://nf-co.re/eager/2.5.3/docs/output/#general-stats-table I believe it is the reads before/reads after deduplication. My best guess is that since nf-core/eager does bam filtering before deduplication, if you have applied any filters to your bams (e.g. Q30), that might affect the number of reads before DeDup, and hence the reported number.