Filter fastq files
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2.6 years ago
ATCG ▴ 370

After removing over-represented sequences using trimmomatic my fasq file has a large number of small sequences. How can I remove these using trimmomatic if possible or other tools except awk.

Fastq trimmomatic • 589 views
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This will work cutadapt --minimum-length 20 -o output.fastq input.fastq

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Try bbduk.sh in future. A guide is available here. Easy to understand options, fast.

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2.6 years ago

Consult the Trimmomatic manual

http://www.usadellab.org/cms/?page=trimmomatic

you will need to use the MINLEN action

or as seen in the manual

java -jar trimmomatic-0.39.jar PE 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 MINLEN:36

yikes for user interface. So I'd recommend using another tool.

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