5. Trimming

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We will use Trimmomatic for read trimming and filtering, and adapters removal.

Let’s see its general usage. To run trimmomatic you need to specify its full path: /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar): 

$ java -jar /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar -h

Usage: 

 PE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-basein <inputBase> | <inputFile1> <inputFile2>] 
      [-baseout <outputBase> | <outputFile1P> <outputFile1U><outputFile2P> <outputFile2U>] <trimmer1>...

or: 

SE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] <inputFile> <outputFile> <trimmer1>...
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