phap/phred : using fastq quality

[Meligethes]

Hi,

Is there any way phrap uses fastq quality ?

In manuals and over the internet no results found :s

Thx for your help

[sklages]

What do you exactly mean? AFAIR phrap uses fasta/qual.

[Meligethes]

I would like to use phrap with quality values.
But the only quality i have is in fastq format.
Phrap with fastq input file returns error as sequences don't begin with ">" (but "@"). Thus, how can I convert fastq files to be used by phrap (WITH quality)?

[sklages]

AFAIR phrap only uses fasta/qual.

Convert your fastq to fasta/qual with your tool of choice (e.g. convert_project from MIRA assembler package) and then feed phrap with the resulting fasta/quals.

Have a look at http://phrap.org/phredphrap/phrap.html (3. Quality files.)

The name of this file must consist of the name of the FASTA file, with ".qual" appended.

The online docs are quite old but there is a README shipped with the Phrap software distribution which contains more up-to-date info.

hth, Sven