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UMI tags can't be add to reads name properly while pair end mode
Thanks for your brilliant work! flexbar is my most used trimming tool. But I found a little defect recently when enabling --umi-tags. The UMI would be added behind reads number but reads name, like this @E100047096L1C001R0030000415/2_TGCACGAGAC. So I need to use some tools like bioawk to relocate the UMI tags otherwise they will be ignored by mapping tools or cause the error. Maybe you can add some identify pattern options and let UMI tags add correctly?