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

Chris Fields cjfields at illinois.edu
Tue Jul 27 11:57:43 EDT 2010


On Jul 27, 2010, at 10:34 AM, Peter wrote:

> On Tue, Jul 27, 2010 at 3:55 PM, Alan Twaddle <twaddlac at gmail.com> wrote:
>> I'm not certain that I'm using the latest BioPerl, but I can check. In
>> the mean time, I'll send you the example data!
>> 
>> @FQ4HLCS02EO12Q region=2 tag=H
>> +GCGAAGAACCTTACCTACTCTTGACATCCAGAGAATTCGCTAGAGATAGCTTAGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGAGTAATGTCGGGAACTCAAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAACTCATCATGCCCCTTGCTGATAC
>> +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIID666IIIIHHHIIIIIIHHHIIIIIIIIIIDCCHHHIIIIIIGGGIIIIIIIIIIIHHHIIIHH???HHIII???IIIIIIIIIIIIIIIIHHHIIIIIIIIIIIICC@@HIIIIIIIIIIGEGGGGG?4444CCIIIGGGII
>> @FQ4HLCS02EO12T region=2 tag=B
>> +GATGAATTGACGTCATCCCCACCTTCCTCCGGTTTATTACCGGCAGTCTCGCTAGAGTGCCCAACTAAATGATGGCAACTAACAATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCACCACCTGTCACTTTGTCCCCGAAGGGAACTTCTATCTCTAGAAGGGTCAAAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCAATTCGATGTCGAGC
>> +DDDGDGGGIIIIIIII@@@@IIIIIIIIIIIIHHB985DFI<<;==DDDGDBDADBG=644466AGB==GDEEFHHEEEHHHHHHHH====GE=D<<<;DBGED;;;;:9955000247<;;;;DGGGGHHHHHBBBHGGGHGGBBB@@@@>;;666EGGEEBBDD<97550//4--,,.62426468=ADD>>6666BBDDEEAEGEG;;;B>@@B;266;;GGDBA?:::995/////9>>9989=9:5
>> 
> 
> Hopefully this is just an email problem, but that doesn't look like a
> well formatted
> FASTQ record to me. Where is the "+" line separating the sequence and qualities?
> 
> Maybe sending this single record as an attachment would work better (is that
> encouraged on this mailing list?).
> 
> Peter

As long as the attachment isn't many MB in size, I don't have a problem.  Might get delayed by any spam filters though.

chris




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