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general:computerenvironment:software:trimmomatic [2021/04/21 08:07] – [Trimmomatic] felixgeneral:computerenvironment:software:trimmomatic [2024/05/19 13:40] (current) – [Example program call] freya
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 You can start your Trimmomatic run via a command line call where you specify the names of the input files together with the tasks and the parameter settings that tell Trimmomatic how the clipping should be performed. **Be careful**,** the tasks that you pass on to Trimmomatic must not be in an arbitrary order**. This is, because Trimmomatic will perform the tasks exactly in the order as it is specified in the command line call. If this is not obeyed, the trimming results might deviate in part substantially from what you had in mind. You can start your Trimmomatic run via a command line call where you specify the names of the input files together with the tasks and the parameter settings that tell Trimmomatic how the clipping should be performed. **Be careful**,** the tasks that you pass on to Trimmomatic must not be in an arbitrary order**. This is, because Trimmomatic will perform the tasks exactly in the order as it is specified in the command line call. If this is not obeyed, the trimming results might deviate in part substantially from what you had in mind.
 ==== Example program call ==== ==== Example program call ====
- +'' 
-java -jar <yourversionoftrimmomatic>.jar PE -phred33 <Inputfile-Forward>.fq <Inputfile-Reverse>.fq <Inputfile-Forwared_trimm_paired>.fq.gz <Inputfile-Forward_trimm_unpaired>.fq.gz <Inputfile-Reverse_trimm_paired>.fq.gz <Inputfile-Reverse_trimm_unpaired>.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36+trimmomatic PE -phred33 <Inputfile-Forward>.fq <Inputfile-Reverse>.fq <Forward_trimm_paired>.fq.gz <Forward_trimm_unpaired>.fq.gz <Reverse_trimm_paired>.fq.gz <Reverse_trimm_unpaired>.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 
 +''
  
 ==== The options ==== ==== The options ====