filtering the reads based on the length
I have a fastq file (RNAseq) and filtered the linkers. now the sequences in the file have different length. I want to remove the reads with shorter than 21 nucleotide and use the rest of the reads. do you know any toll to do that?
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geocarvalho
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alireza346 •
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alireza346 •
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Use the following tool from BBMap suite. reformat.sh in=your_fq.gz out=filt.fq.gz minlength=21. (Note: If you have paired-end data you will need to use in1= in2= and out1= out2=).
Another great option is fastp:
fastp --length_required 30 -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz
You may include --detect_adapter_for_pe if adapters are still there, --compression, --thread, and --html for a report.
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How did you remove the adapters (linkers)? I hope you used an established tool like
Cutadapt. These tools have in-built options to discard reads shorter a given threshold.Hi,
You can use fastaparse.pl script available in mirdeep2 package.
Does that script work with
fastqformat files? OP is specifically asking about that format.Filtering Fastq Sequences Based On Lengths