java -jar /home/liuhui/bin/trinityrnaseq_r20140413p1/trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads 20 -phred33 P_ACAGTG_L002_R1_001.fastq.gz P_ACAGTG_L002_R2_001.fastq.gz \
P_ACAGTG_L002_R1_001.fastq.gz.P.qtrim P_ACAGTG_L002_R1_001.fastq.gz.U.qtrim P_ACAGTG_L002_R2_001.fastq.gz.P.qtrim P_ACAGTG_L002_R2_001.fastq.gz.U.qtrim SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25
cat P_ACAGTG_L002_R1_001.fastq.gz.P.qtrim P_ACAGTG_L002_R1_001.fastq.gz.U.qtrim > P_ACAGTG_L002_R1_001.fastq.gz.PwU.qtrim.fq
cat P_ACAGTG_L002_R2_001.fastq.gz.P.qtrim P_ACAGTG_L002_R2_001.fastq.gz.U.qtrim > P_ACAGTG_L002_R2_001.fastq.gz.PwU.qtrim.fq
gzip P_ACAGTG_L002_R1_001.fastq.gz.P.qtrim P_ACAGTG_L002_R1_001.fastq.gz.U.qtrim P_ACAGTG_L002_R2_001.fastq.gz.P.qtrim P_ACAGTG_L002_R2_001.fastq.gz.U.qtrim &
转载于:https://www.cnblogs.com/liuhui0622/p/4689910.html