![]() ![]() ![]() # Trimming Paired-End (PE) reads:perl -tm /usr/local/bin/trimmomatic-0.33.jar -d PE -fq FileNameSeed -t 10 -ph 33 -ad TruSeq3-PE.fa:2:30:10 -l 30 -sl 4:30 -tr 30 -m 32# Trimming Single-End (SE) reads:perl -tm /usr/local/bin/trimmomatic-0.33.jar -d SE -fq FileNameSeed -t 10 -ph 33 -ad TruSeq3-SE.fa:2:30:10:true -l 30 -sl 4:30 -tr 30 -m 32If the Illumina adaptors were successfully removed by Script 1, you may disable Trimmomatic's 'ILLUMINACLIP' option by simply setting -ad to 0. Ex: CGG (MspI)String-tNumber of independent threads used by Parallel::ForkManagerNumeric10UNIX command examples. Ex: TGCA (PstI)String-enz2Enzyme 2 restriction site residue sequence. Ex: FileNameSeedR10 34.fastq.gzNumeric-enz1Enzyme 1 restriction site residue sequence. Ex: FileNameSeedR100 1.fastq.gzNumeric-eEnd number of FASTQ files.
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