55 lines
1.6 KiB
Bash
55 lines
1.6 KiB
Bash
#!/bin/bash
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#
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# Reference: http://www.usadellab.org/cms/?page=trimmomatic
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module load Trimmomatic
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PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
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FASTQ_OUT="${PROJECT_DIRECTORY}/step2/"
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mkdir -p "${FASTQ_OUT}"
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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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# Trimmomatic example Paired end data.
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#
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# Flags:
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# - ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the
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# read.
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# - SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average
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# quality within the window falls below a threshold.
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# - LEADING: Cut bases off the start of a read, if below a threshold quality.
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# - TRAILING: Cut bases off the end of a read, if below a threshold quality.
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# - HEADCROP: Cut the specified number of bases from the start of the read.
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# - MINLEN: Drop the read if it is below a specified length.
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java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar PE \
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-phred33 \
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sample1_R1.fastq.gz \
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sample1_R2.fastq.gz \
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"${FASTQ_OUT}/sample1_R1_paired.fastq.gz" \
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"${FASTQ_OUT}/sample1_R1_unpaired.fastq.gz" \
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"${FASTQ_OUT}/sample1_R2_paired.fastq.gz" \
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"${FASTQ_OUT}/sample1_R2_unpaired.fastq.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 data.
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java -jar $EBROOTTRIMMOMATIC/trimmomatic.jar SE \
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-phred33 \
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sample1.fastq.gz \
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output.fastq.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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