forked from GRIAC/system_genetics
42 lines
872 B
Bash
42 lines
872 B
Bash
#!/bin/bash
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# reference: http://www.usadellab.org/cms/?page=trimmomatic
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module load Trimmomatic
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# Adapters can be found at
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# https://github.com/timflutre/trimmomatic/tree/master/adapters
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# But should be verified with FastQC, or in another way.
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# (Example) Paired end
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java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
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-phred33 \
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input_forward.fq.gz \
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input_reverse.fq.gz \
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output_forward_paired.fq.gz \
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output_forward_unpaired.fq.gz \
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output_reverse_paired.fq.gz \
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output_reverse_unpaired.fq.gz \
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ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 \
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LEADING:3 \
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TRAILING:3 \
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SLIDINGWINDOW:4:25 \
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HEADCROP:8 \
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MINLEN:50
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# (Example) Single end
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java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar SE \
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-phred33 \
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input.fq.gz \
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output.fq.gz \
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ILLUMINACLIP:TruSeq3-SE:2:30:10 \
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LEADING:3 \
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TRAILING:3 \
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SLIDINGWINDOW:4:15 \
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HEADCROP:8 \
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MINLEN:50
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