[BioC] fastq files

[Martin Morgan]

On 03/11/2011 05:42 AM, David martin wrote:
> Hi,
> I have the following fastq header:
> 
> @ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1
> NGGGCTGGGTCGGTCGGGC
> +ILLUMINA-E6F4B9_0000:5:1:1184:949#0/1
> BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
> 
> Does any of the R packages (e.g: shortread) can convert this fastq to
> fasta file ?

Hi David --

In Biostrings

  write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile)

in ShortRead

  writeFasta(readFastq(fromFile), toFile)

both read the entire file into memory.

Martin

> 
> thanks,
> david
> 
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