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Old 06-30-2009, 09:15 AM   #1
aritakum
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Location: TN

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Posts: 5
Default Split GA FASTQ file

Does anyone have a script to split FASTQ file into fasta seqeucne file and fasta quality file?

I have tried fq_all2std.pl from MAQ and it converts fastq to sequence fasta just fine, but it throws the following errors when I try otehr options
export2std:
Use of uninitialized value $t[21] in string eq at ./fq_all2std.pl line 177, <> line 1.
export2sol
Use of uninitialized value $t[21] in string eq at ./fq_all2std.pl line 164, <> line 1.

Thanks

Am
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Old 06-30-2009, 11:44 AM   #2
kmcarr
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Default

Am,

The export2std or export2sol are not appropriate when your input is FASTQ, that is why it is throwing errors. To split a FASTQ into FASTA sequence and quality files you should use the 'std2qual' sub command of fq_all2std. This will take a FASTQ file and output one .seq file and one .qual file. The syntax is:

fq_all2std std2qual <out_prefix> <input_fastq>

The out_prefix will form the first part of the output filenames, e.g. out_prefix.seq and out_prefix.qual.

The script assumes that the FASTQ quality scores are encoded using the standard Sanger method (i.e. Phred+33). If the FASTQ file is using Solexa encoding (Phred+64) you first need to convert the FASTQ using:

fq_all2std sol2std <input_fastq> > output.fastq
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Old 06-30-2009, 12:11 PM   #3
aritakum
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Default splita GA fASTQ

Hi,
The fq_all2std.pl I have does not recognize std2qual!

Here is the top few lines form the code ....

fq_all2std.pl
#!/usr/bin/perl -w
# Author: lh3
# Version: 0.1.6

use strict;
use warnings;
use Getopt::Std;

my $usage = qq(
Usage: fq_all2std.pl <command> <in.txt>

Command:
scarf2std Convert SCARF format to the standard/Sanger FASTQ
fqint2std Convert FASTQ-int format to the standard/Sanger FASTQ
sol2std Convert Solexa/Illumina FASTQ to the standard FASTQ
fa2std Convert FASTA to the standard FASTQ
seqprb2std Convert .seq and .prb files to the standard FASTQ
fq2fa Convert various FASTQ-like format to FASTA
export2sol Convert Solexa export format to Solexa FASTQ
export2std Convert Solexa export format to Sanger FASTQ
csfa2std Convert AB SOLiD read format to Sanger FASTQ
instruction Explanation to different format
example Show examples of various formats

Note: Read/quality sequences MUST be presented in one line.
......................rest deleted........

_________________________________________________________________________________

Never mind, I found std2qual in the new release of MAQ!

THANKS

Last edited by aritakum; 06-30-2009 at 12:26 PM. Reason: Found a solution
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Old 06-10-2010, 05:15 AM   #4
robertorun
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Location: wuhan,China

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Posts: 22
Default

It's a good tool. I have use it!
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