I got an error:
> names(sr) <- id(fq)
Error in `names<-`(`*tmp*`, value = <S4 object of class "BStringSet">) : 
  'value' must be NULL or a character vector





________________________________
From: Martin Morgan <mtmorgan@fhcrc.org>

Cc: bioc-sig-sequencing@r-project.org
Sent: Monday, August 3, 2009 7:06:56 PM
Subject: Re: [Bioc-sig-seq] fastq2fasta

Hi Joseph --

One way, for some file 'fin' to file 'fout'

fq <- readFastq(fin)
sr <- sread(fq)
names(sr) <- id(fq)
write.XStringSet(sr, fout, format="fasta")

Martin

joseph wrote:
> Hello
> Can you show me how to use ShortRead to convert a fastq file  like this one 
> @7:1:1
> NNNNNNN
> +
> %%%%%%
> @7:1:2
> NNNNNNN
> +
> %%%%%%
> 
> to a fasta file keeping only the id and the read:  
> 
>> @7:1:1
> NNNNNNNN
>> @7:1:2
> NNNNNNNN
> 
> Thanks in advance
> Joseph
> 
> 
>      
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> 
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