Hi,
I am trying to run paired end trimming with cutadapt 1.12 so STAR aligner won't complain that the two read files are not the same, but somehow it won't run with the command structure that is given in the manual:
cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq reads.1.fastq reads.2.fastq
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC —A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o NS2521_S1_R1noadapt.fastq -p NS2521_S1_R2noadapt.fastq NS2521_S1_R1_001.fastq NS2521_S1_R2_001.fastq
but all I get is "cutadapt: error: Too many parameters." no matter if i have options in there or not
Going crazy - what am I doing wrong???
Thanks,
Danielle
I am trying to run paired end trimming with cutadapt 1.12 so STAR aligner won't complain that the two read files are not the same, but somehow it won't run with the command structure that is given in the manual:
cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq reads.1.fastq reads.2.fastq
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC —A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o NS2521_S1_R1noadapt.fastq -p NS2521_S1_R2noadapt.fastq NS2521_S1_R1_001.fastq NS2521_S1_R2_001.fastq
but all I get is "cutadapt: error: Too many parameters." no matter if i have options in there or not
Going crazy - what am I doing wrong???
Thanks,
Danielle
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