Biostar Beta. Not for public use.
trimmomatic: command not found
0
Entering edit mode
10 months ago
SeaStar • 10
Ocean

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?

ADD COMMENTlink
1
Entering edit mode

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.

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1