[Bioperl-l] How to Obtain Nucleotide Sequence from SeqIO::fastq

Alan Twaddle twaddlac at gmail.com
Tue Jul 27 10:38:09 EDT 2010


On Tue, Jul 27, 2010 at 10:16 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com> wrote:
> Hi Alan,
>
> Another case for the deobfuscator:
> http://bioperl.org/cgi-bin/deob_interface.cgi
>
> A Bio::Seq::Quality object is a Bio::PrimarySeq, so you can just say
> $seqqual->seq to get the sequence as a string.
>
> Cheers.
> Roy.
>
> On 27/07/2010 15:10, Alan Twaddle wrote:
>>
>> Hello,
>>
>>      I am curious as to how I am supposed to use SeqIO::fastq to read
>> in a fastq file and then obtain the nucleotide sequence from that. I
>> noticed that SeqIO::fastq returns a Seq::Quality object but I haven't
>> seen a method within that module that returns the nucleotide sequence.
>> Please, let me know if you have any suggestions!
>>
>> Thank you very much!!
>>
>
>



-- 

Alan Twaddle, B.S.
MUC class of 2010



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