Question: filtering the reads based on the length
0
gravatar for alireza346
8 months ago by
alireza3460
alireza3460 wrote:

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 • 658 views
ADD COMMENTlink modified 8 months ago by karthic100 • written 8 months ago by alireza3460

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.

ADD REPLYlink written 8 months ago by ATpoint16k

Hi,

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

ADD REPLYlink written 8 months ago by karthic100

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

ADD REPLYlink written 8 months ago by genomax67k

Filtering Fastq Sequences Based On Lengths

ADD REPLYlink written 8 months ago by Pierre Lindenbaum120k
0
gravatar for genomax
8 months ago by
genomax67k
United States
genomax67k wrote:

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=).

ADD COMMENTlink modified 5 weeks ago • written 8 months ago by genomax67k
0
gravatar for cpad0112
8 months ago by
cpad011211k
India
cpad011211k wrote:

Try with seqkit:

seqkit seq -m 21 in.fq/in.fastq
ADD COMMENTlink written 8 months ago by cpad011211k
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