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
That shouldn't actually be possible. Are you sure that you didn't either merge two BAM files or that you're actually filtering for MAPQ>10?