convert FASTA into FASTQ using linux
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9.7 years ago
rhoney45 ▴ 20

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

sequence • 31k views
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5.6 years ago
GenoMax 143k

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

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9.7 years ago
Manvendra Singh ★ 2.2k

There is a perl script here

Usage is

perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq
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Note: This assumes a qual score of 40. Nice tool though!

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

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

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

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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

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See A: Convert from fasta to fastq for an alternative

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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)

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9.7 years ago
Ram 44k

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.

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