[BioC] fastq files

[Martin Morgan]

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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