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

Peter biopython at maubp.freeserve.co.uk
Tue Jul 27 11:34:11 EDT 2010


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


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