The original code only exclude the UNMAP reads from calculating edit efficiency of on/off targets, I think we should exclude the following reads as well .
SECONDARY: this is not a primary mapping position of this read.
QCFAIL: QC failed reads should be dropped.
DUP: duplicated reads should be dropped.
SUPPLEMENTARY: this is not the major mapping part of this read.
I think use the above reads might lead to some misleading of the calculation.
The original code only exclude the UNMAP reads from calculating edit efficiency of on/off targets, I think we should exclude the following reads as well . SECONDARY: this is not a primary mapping position of this read. QCFAIL: QC failed reads should be dropped. DUP: duplicated reads should be dropped. SUPPLEMENTARY: this is not the major mapping part of this read. I think use the above reads might lead to some misleading of the calculation.