[Bioc-sig-seq] fastq2fasta

[Martin Morgan]

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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