Question: filtering the reads based on the length
0
gravatar for alireza346
20 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 • 1.6k views
ADD COMMENTlink modified 20 months ago by karthic100 • written 20 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 20 months ago by ATpoint34k

Hi,

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

ADD REPLYlink written 20 months ago by karthic100

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

ADD REPLYlink written 20 months ago by genomax83k

Filtering Fastq Sequences Based On Lengths

ADD REPLYlink written 20 months ago by Pierre Lindenbaum128k
0
gravatar for genomax
20 months ago by
genomax83k
United States
genomax83k 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 13 months ago • written 20 months ago by genomax83k
0
gravatar for cpad0112
20 months ago by
cpad011213k
India
cpad011213k wrote:

Try with seqkit:

seqkit seq -m 21 in.fq/in.fastq
ADD COMMENTlink written 20 months ago by cpad011213k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1114 users visited in the last hour