converting_fastq_file

[angelpie]

I have illumina v1.5+ type fastq files.

I learned fastq file consists of 4 types, sanger, illumina v1.0, v1.3 and v1.5.
Then, I also learned many programs require sanger type fastq files.

Method of converting illumina v1.0 (solexa) into sanger is found occasionally.
However, I can't find actual procedures of converting illumina v1.5 into sanger.

Could you please help me?

[nicolallias]

Hi,
The only difference between those formats is the quality, if you are familiar with Perl, try the following :

http://seqanswers.com/forums/showthread.php?t=5192

$q_line =~ tr/\x40-\xff\x00-\x3f/\x21-\xe0\x21/;

Which could be written in Python as
q_line = "".join([chr(ord(i)-31) for i in q_line])

Or do you prefer an awk line ?
Or a full script ready-to-use ?

[maubp]

Could you please help me?

See http://en.wikipedia.org/wiki/FASTQ_format and:

Cock et al (2009) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, http://dx.doi.org/10.1093/nar/gkp1137

From the point of view of conversion, FASTQ files from Illumina 1.5 are basically the same as Illumina 1.3 and 1.4 except the meaning of some low qualities, see:

http://seqanswers.com/forums/showpost.php?p=17491&postcount=3

http://news.open-bio.org/news/2010/04/illumina-q2-trim-fastq/

[angelpie]

Thank nicolallias and maubp for your quick reply.

Although I think I know formulae of these formats,
I don't know how do I convert between them
because I am just a user of existent scripts/programs.

Can I use procedures for illumina v1.3 to convert illumina v1.5+ files?

I tried to use perl script in refered thread.
However, I found errors.

Or a full script ready-to-use ?

If possible, please teach me.

[maubp]

Can I use procedures for illumina v1.3 to convert illumina v1.5+ files?

Yes.

I am just a user of existent scripts/programs.

Try EMBOSS seqret if you want a command line tool for converting file formats. Use fastq-illumina as the input format, fastq-sanger as the output format.

If you are happier with Python, Perl, Java, or Ruby then try Biopython, BioPerl, BioJava or BioRuby for existing libraries for reading, writing and converting FASTQ files (see the paper I linked to before).

I tried to use perl script in refered thread.
However, I found errors.

What errors?

[angelpie]

Error messages said
"Use of uninitialized value $(variables) in concatenation (.) or string at .....".

[maubp]

I don't know enough Perl to help you - but I don't think nicolallias' example was standalone, it was more of a hint for someone familiar with Perl.

Do you have EMBOSS installed? The EMBOSS tool seqret is an easy way to do this at the command line.

[nicolallias]

it was more of a hint for someone familiar with Perl

Exact, and using already written tools is your best option.
angelpie: if you wish to learn more, you really should visit the wikipedia page about Fastq format.

[epigen]

convert Illumina scores to Phred in a BAM file

If you already have a BAM file, you can transform the scores in it as follows:

samtools view -h Illumina_score.bam | perl -lane '$"="\t"; if (/^@/) {print;} else {$F[10]=~ tr/\x40-\xff\x00-\x3f/\x21-\xe0\x21/;print "@F"}' | samtools view -Sbh - > Phred_score.bam

Thanks nicolallias for providing the very efficient trick. It saved us a lot of fastq file transformations and we did not have to run all the BWA alignments again.