system_genetics/rnaseq/step2_trim/snippet.sh

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