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general:computerenvironment:software:trimmomatic [2019/01/10 14:02] – external edit 127.0.0.1general:computerenvironment:software:trimmomatic [2024/05/19 13:40] (current) – [Example program call] freya
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 Trimmomatic is one of the many software tools for clipping low quality regions as well as adapter sequences from DNA sequencing reads. It is part of the Trinity standard workflow for RNA seq assembly. However, please note that this is by no means a guarantee that Trimmomatic is the all time optimal tool for sequence read pre-processing. Trimmomatic can be run both in single end and in paired end mode. Figure {{ref>TM}} outlinese the workflow for the paired end mode. Trimmomatic is one of the many software tools for clipping low quality regions as well as adapter sequences from DNA sequencing reads. It is part of the Trinity standard workflow for RNA seq assembly. However, please note that this is by no means a guarantee that Trimmomatic is the all time optimal tool for sequence read pre-processing. Trimmomatic can be run both in single end and in paired end mode. Figure {{ref>TM}} outlinese the workflow for the paired end mode.
  
-<figure TM> {{:wiki:mbw:trimmomatic-pe-workflow.png?400  |Trimmomatic workflow for paired end mode}}<caption><fs 0.8em>Flow of reads in Trimmomatic paired end mode. The software expects the two reads of a read pair to be stored in separate files. Once the trimming is completed, Trimmomatic will generate four output files, again separate files for the forward and the reverse reads. Figure source: {{:wiki:mbw:literature:trimmomaticmanual_v0.32.pdf|Trimmomatic manual V0.32}}.</fs></caption> </figure>+<figure TM> {{ :general:computerenvironment:software:trimmomatic.png?500 |}}<caption><fs 0.8em>Flow of reads in Trimmomatic paired end mode. The software expects the two reads of a read pair to be stored in separate files. Once the trimming is completed, Trimmomatic will generate four output files, again separate files for the forward and the reverse reads. Figure source: [[http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf|Trimmomatic manual V0.32]].</fs></caption> </figure>
  
 ===== Running Trimmomatic ===== ===== Running Trimmomatic =====
  
-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 Trinity 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 ====
  
-Below you find a number of common options. For full details please have a look at the {{ :wiki:mbw:literature:trimmomaticmanual_v0.32.pdf |Trimmomatic manual}}.+Below you find a number of common options. For full details please have a look at the [[http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf|Trimmomatic manual]].
  
   * **PE**: you provided reads of a paired end library.   * **PE**: you provided reads of a paired end library.