[BioC] fastq files

[David martin]

Cool,
thanks

On 03/11/2011 03:10 PM, Martin Morgan wrote:
> On 03/11/2011 06:06 AM, David martin wrote:
>> 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 ?
>
> Type read. and then tab key -- correct is read.DNAStringSet /
> write.XStringSet, sorry. Martin
>
>>
>>
>>
>>
>>
>> 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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>>>
>>
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>
>