trimmomatic: command not found

Question

[n_navy]

Hello I'am super new in Bioinformatics and I'm trying to do trimming in RNA-Seq data on Ubuntu. -I'm using Windows-

I downloaded Trimmomatic, and check by:

ls Trimmomatic-0.39

Results;

LICENSE adapters trimmomatic-0.39.ja

But when I run this:

trimmomatic PE -phred33 SRS3773142_1.fastq SRS3773142_2.fastq \ SRS3773142_1_paired.fastq.gz SRS3773142_1_unpaired.fastq.gz \ SRS3773142_2_paired.fastq.gz SRS3773142_2_unpaired.fastq.gz \ ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

It gives error:

trimmomatic: command not found

Can you help me?

Answer 1

[Michael]

Trimmomatic is a java program, so you have to invoke it like java -jar trimmomatic-0.39.jar if you didn't install the wrapper script in your PATH. You need to study the basics of the Unix command line (irrespective of using WSL in Windows or native Linux) before you proceed, otherwise, proper analysis of complex bioinformatics data will not be possible. A few further recommendations:

• Use Conda/Bioconda for installing your software (that would probably have installed the wrapper in the right place, not sure whether there is one in this case)
• A proper setup of your computer is described in the Biostars handbook
• I wouldn't use trimmomatic any more, it has been superseded by other tools. Try fastp instead, it is easier to use and does QC and trimming in one go. Most recent Illumina data should not need much trimming.

[n_navy]

Thanks for advices. I tried java -jar trimmomatic-0.39.jar, but gives: Unable to access jarfile trimmomatic-0.39.jar

Unfortunately, I have to use trimmomatic for my project. So what else I can do with this error?

[Michael]

I guess you are issuing the command in the wrong directory. You should spend some time on Linux/Unix basics first. Tasks like changing directories, finding executables, and defining the PATH are very essential tasks that everyone has to master before doing bioinformatics (at least those who want to work on the command line). Without the basics, you cannot perform any of your analyses successfully.

[bhumm]

I agree with michael that you are executing in the wrong directory - you can use which trimmomatic to find the directory where it is installed. As michael also stated, I would use Conda/Bioconda to install it so you can call the program from anywhere using the wrapper.