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Old 04-18-2016, 01:44 AM   #1
Areeya
Junior Member
 
Location: Thailand

Join Date: Apr 2016
Posts: 1
Default Trimmomatics output files

Why I could get only paired and unpaired files of R1 but not those R2 when I run the below command in Trimmomatics?

Command line for batch analysis in Trimmomatics:

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
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Old 04-18-2016, 09:34 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Using the variable 'o' for your R2 output file names. Nothing to do with trimmamatic but rather your script.
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