Hi everyone! I've encountered an interesting discrepancy when trying to filter the results of my paired end CHIP-SEQ. When using bowtie2 in Galaxy interface it is shown how many mapped, uniquely mapped and more than once mapped reads were found. When I filter the Bowtie2 results, leaving only reads that were mapped in a proper pair and with MAPQ >10 ( I understood MAPQ>10 is supposed to be a good enough filter to use in this case) I stay with more reads than uniquely plus non-uniquely mapped reads, which doesn’t make any sense. For example: The number of all reads is 3,864,595, The number of all mapped reads (uniquely+ more than once) is 2,156,879 The number of properly paired, MAPQ>10 reads is 2,374,371

Does anybody have any explanation for this? Thank you! Yulia