Question: convert FASTA into FASTQ using linux
2
gravatar for rhoney45
6.3 years ago by
rhoney4520
United Kingdom
rhoney4520 wrote:

Hiiii....If anyone can please helo me how to convert fasta files into fastq using ubuntu....i shall be very thank ful....

sequence • 25k views
ADD COMMENTlink modified 2.2 years ago by GenoMax96k • written 6.3 years ago by rhoney4520
9
gravatar for GenoMax
2.2 years ago by
GenoMax96k
United States
GenoMax96k wrote:

For those who may happen to reach this thread by way of search in future you can convert a fasta file to fastq format using reformat.sh from BBMap suite.

Please remember that the Q-scores created here are fake (example below sets Q-scores to 35 for all bases).

reformat.sh in=test.fa out=fake.fq qfake=35

ADD COMMENTlink written 2.2 years ago by GenoMax96k
8
gravatar for Manvendra Singh
6.3 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

There is a perl script here

Usage is

perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq
ADD COMMENTlink modified 2.2 years ago by Ram32k • written 6.3 years ago by Manvendra Singh2.1k

Note: This assumes a qual score of 40. Nice tool though!

ADD REPLYlink written 6.3 years ago by Ram32k

very nice script, Thank you so much! It also works on Mac!

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by yeningrong00

please, the qual string length is one base longer than the sequence length. Could you advise how to solve it?

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by hpatzenhauerova10

Paste your sequence and qual strings here - maybe that will help figure out what's happening.

ADD REPLYlink written 3.5 years ago by Ram32k

Hi! The script works unless I use warnings; If I use it, then it gives a warning:

Use of uninitialized value $header in string ne at fasta_to_fastq.pl line 13, <FILE> line 1.

In line 13 is:

if($header ne "") {

Thank you in advance

ADD REPLYlink modified 2.2 years ago by Ram32k • written 2.2 years ago by katerinavram0

See A: Convert from fasta to fastq for an alternative

ADD REPLYlink written 2.2 years ago by WouterDeCoster45k

You'll have to add my $header; somewhere at the top op the script (aka, declare the variable). I would also advise to add use strict; (next to use warnings)

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by lieven.sterck10k
6
gravatar for Ram
6.3 years ago by
Ram32k
Baylor College of Medicine, Houston, TX
Ram32k wrote:

Hi,

FASTQ has more information content than FASTA. The conversion would require that you add some kind of quality scores, most probably some dummy values.

What would really enable us help you better is knowing the purpose behind your quest.

ADD COMMENTlink written 6.3 years ago by Ram32k
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