trimmomatic: command not found
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2.9 years ago
SeaStar ▴ 50

hello, I'm new here. I was using trimmomatic and I put this commands,

 trimmomatic PE -phred33 testadapt.1.fastq testadapt.2.fastq test_trim_paired.1.fq.gz testes_trim_unpaired.1.fq.gz test_trim_paired.2.fq.gz test_trim_unpaired.2.fq.gz ILLUMINACLIP:/home/lab/Software/Trimmomatic-0.38/adapters/NexteraPE-PE.fa:2:30:10:4 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

but it reminds to me

trimmomatic: command not found

Any helps?

trimming software error • 3.1k views
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How did you install Trimmomatic? It is a Java program, and according to the manual, it should be used with:

java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> output> <step 1> ...

If you are using Ubuntu / Debian and installed from the distro repository, there are two wrappers: TrimmomaticPE and TrimmomaticSE.

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Program is not installed or is not in system path (your shell path). SeaStar

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