Filter fastq files

Question

[ATCG]

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.

[Pierre Lindenbaum]

Filtering Fastq Sequences Based On Lengths

[ATCG]

This will work cutadapt --minimum-length 20 -o output.fastq input.fastq

[GenoMax]

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

Answer 1

[Istvan Albert]

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.