Adapter trimming
- Input read pairs Total number of read pairs in the fastq files.
- Read pairs discarded by adapter trimming Trimmed read pairs, that after trimming are shorter than specified in the option "Minimum read length after adapter trim" and have been discarded.
- Read pairs trimmed by adapter trimming Read pairs that have been trimmed and are longer than "Minimum read length after adapter trim".
- R1 reads trimmed by adapter trimming Trimmed R1 reads that are longer than "Minimum read length after adapter trim".
- R2 reads trimmed by adapter trimming Trimmed R2 reads that are longer than "Minimum read length after adapter trim".
- Average read length before adapter trimming Average length of the reads before adapter trimming. If quality trimming was enabled, read length after quality trim is given.
- Average read length after adapter trimming Average read length after adapter trimming. This read length may be longer than Average read length before adapter trimming because short reads can have been discarded.
- Detected R1 adapter The consensus sequence of bases removed from R1 reads.
- Detected R2 adapter The consensus sequence of bases removed from R2 reads.
The plot Read lengths of adapter trimmed reads before / after trimming shows the number of reads as a funtion of read length before and after adapter trimming (figure 12.2).
Figure 12.2: The number of reads as a function of read length before and after adapter trimming.
The plot Lengths of trimmed adapters shows the number and lengths of trimmed adapter sequences (figure 12.3).
Figure 12.3: The number and length of trimmed adapter sequences.