The command for batch analysis in Trimmomatic
for A in WMB*_R1.fastq ;
do B=${A%%_R1.fastq}_R2.fastq;
o=${A#};
o=${o%_R1.fastq};
o1=$o".paired_R1.fastq";
o2=$o".unpaired_R1.fastq";
o=3$o".paired_R2.fastq";
o=4$o".unpaired_R2.fastq";
java -jar jars/trimmomatic-0.32.jar PE -phred33 $A $B $o1 $o2 $o3 $o4 ILLUMINACLIP:Trueseq_PE.fa:2:30:10:1:true LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:75; done
Jorge Luis Perez-Moreno
You should change
o=3$o".paired_R2.fastq";
o=4$o".unpaired_R2.fastq";
to
o3=$o".paired_R2.fastq";
o4=$o".unpaired_R2.fastq";
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