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Paired end commands are a little more complicated: It's a multi step process: first providing both R1 and R2 files to create tmp files which are input to the second cutadapt command.
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/corral-repl/utexas/BioITeam/bin/cutadapt-1.3/bin/cutadapt -a GATCGGAAGAGCACACGTCTGAACTCCA -m 22 --paired-output tmp.2.fastq -o tmp.1.fastq Sample1_R1.fastq Sample1_R2.fastq & /corral-repl/utexas/BioITeam/bin/cutadapt-1.3/bin/cutadapt -a ATCGTCGGACTGTAGAACTCTGAACGTG -m 22 --paired-output trimmed.1.fastq -o trimmed.2.fastq tmp.2.fastq tmp.1.fastq & rm tmp.1.fastq tmp.2.fastq |
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