[BioC] fastq files

[David martin]

library(Biostrings)

fromFile="myfile.fastq"
toFile="output.fa"

 > write.XStringSet(read.XStringSet(fromFile, format="fastq"), toFile)
Error in is(x, "XStringSet") : could not find function "read.XStringSet"

ANy idea ?





On 03/11/2011 02:48 PM, Martin Morgan wrote:
> 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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>
>