Quality trimming
- Input read pairs Total number of read pairs in the fastq files.
- Read pairs discarded by quality trimming Trimmed read pairs, that after trimming are shorter than specified in the option "Minimum read length after quality trim" and have been discarded.
- Read pairs trimmed by quality trimming Read pairs that have been trimmed and are longer than "Minimum read length after quality trim".
- R1 reads trimmed by quality trimming Number of R1 reads trimmed by quality trimming.
- R2 reads trimmed by quality trimming Number of R2 reads trimmed by quality trimming.
- Average read length before quality trimming Average read length of the raw reads in the fastq files.
- Average read length after quality trimming Average read length after quality trimming. This read length may be longer than Average read length before quality trimming because short reads can have been removed.
The plot Read lengths of quality trimmed reads before / after trimming shows the length and number of reads that were quality trimmed before and after trimming (figure 12.1).
Figure 12.1: The number and length of quality trimmed reads before and after quality trimming.