Quality Trimming Via Trimmomatic

已经去除接头(adapter)

java -jar trimmomatic.jar PE -threads 20 -phred33 \
left.fastq.gz right.fastq.gz \
left.Paired.qtrim.fq.gz left.Unpaired.qtrim.fq.gz \
right.Paired.qtrim.fq.gz right.Unpaired.qtrim.fq.gz \
SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:36

### The current trimming steps are:
- Remove leading low quality or N bases (below quality 5) (LEADING:5)
- Remove trailing low quality or N bases (below quality 5) (TRAILING:5)
- Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 5 (SLIDINGWINDOW:4:5)
- Drop reads below the 36 bases long (MINLEN:36) 

cat left.Paired.qtrim.fq.gz left.Unpaired.qtrim.fq.gz > left.PwU.qtrim.fq
cat right.Paired.qtrim.fq.gz right.Unpaired.qtrim.fq.gz > right.PwU.qtrim.fq