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filtering the reads based on the length
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2.3 years ago
alireza346 • 0
@alireza34644789

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?

RNA-Seq • 722 views
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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.

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Hi,

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

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

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21 months ago
genomax 68k
@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=).

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2.3 years ago
@cpad011220673

Try with seqkit:

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