filtering the reads based on the length

Question

[alireza346]

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?

[ATpoint]

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.

[karthic]

Hi,

You can use fastaparse.pl script available in mirdeep2 package.

[GenoMax]

Does that script work with fastq format files? OP is specifically asking about that format.

[Pierre Lindenbaum]

Filtering Fastq Sequences Based On Lengths

Answer 1

[cpad0112]

Try with seqkit:

seqkit seq -m 21 in.fq/in.fastq

Answer 2

[GenoMax]

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=).

Answer 3

[geocarvalho]

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.