Primer trimming
- Mapped read pairs The number of mapped read pairs including specific, non-specific and broken read pairs before UMI grouping.
- Discard read pairs without primer An option used when trimming for primer sequence, can be Yes or No.
- Read pairs without primers Read pairs that could not be assigned to a primer. If "Discard read pairs without primer" is set to yes, these reads will be discarded.
- Primer not found Read pairs not overlapping a primer.
- Inside alignment Read pairs overlapping a primer, but the primer is inside the alignment, not at the end.
- Not enough overlap Read pairs overlapping a primer, but the overlap is less than required as defined in the wizard step "Minimum primer overlap (%)".
- Read too short Read pairs where the remaining sequence of read 1 or read 2 is shorter than the threshold defined in the wizard step "Minimum read length after primer trim".
- Too many read mismatches Read pairs with at least 2 mismatches between the overlapping parts of the read and the primer.
- No primers on chromosome Read pairs mapped to chromosomes where there are no primers.
- Read pairs after primer trimming Read pairs remaining after primer trimming.
- Proper read pairs after primer trimming Read pairs that are mapped as pairs. The percentage is calculated relative to "Read pairs after primer trimming".
- Broken read pairs after primer trimming Mapped read pairs where the distance between the individual reads in the pair exceeded the expected distance for paired reads, or where only one of the reads in the pair was mapped. The percentage is calculated relative to "Read pairs after primer trimming".
- Specific proper read pairs after primer trimming Read pairs that are mapped as pairs and are specific. The percentage is calculated relative to "Read pairs after primer trimming".
- Non-specific proper read pairs after primer trimming Read pairs that are mapped as pairs, but are non-specific. The percentage is calculated relative to "Read pairs after primer trimming".