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Jiri Stiller | 1 Jun 2010 10:03
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Bio::Assembly::Contig object does not contain reads in opposite orientation

Hi,
I am trying to process bam file using Bio::Assembly::IO. I attached test
script and output.
When I am retrieving contigs I get correct contig number and position
but contig objects build from reads of different orientation  don't
contain any read sequences. Contigs built from the reads of the same
orientations are fine.

Your help/advice would be greatly appreciated.

Cheers,

--

-- 
Jiri Stiller
Senior Bioinformatics Researcher
Australian Centre for Plant Functional Genomics
School of Land, Crop and Food Sciences
University of Queensland
Brisbane QLD 4072

j.stiller <at> uq.edu.au
Phone: +61 (0)7 3346 7082
Mobile: +61 (0) 422 941 581
Fax: +61 (0)7 3365 1177


There are [178] contigs in this assembly

CONTIG [sam_assy[KBrB056G23_vs_Bna_03_002_paired:AC189398-KBrB056G23]/101291-101366]
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Mark A. Jensen | 1 Jun 2010 18:36
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Re: Bio::Assembly::Contig object does not contain reads in opposite orientation

Thanks Jiri, I've created a bug report and assigned it to myself. See
http://bugzilla.open-bio.org/show_bug.cgi?id=3088
cheers, Mark
----- Original Message ----- 
From: "Jiri Stiller" <j.stiller <at> uq.edu.au>
To: <bioperl-l <at> bioperl.org>
Sent: Tuesday, June 01, 2010 4:03 AM
Subject: [Bioperl-l] Bio::Assembly::Contig object does not contain reads in 
opposite orientation

> Hi,
> I am trying to process bam file using Bio::Assembly::IO. I attached test
> script and output.
> When I am retrieving contigs I get correct contig number and position
> but contig objects build from reads of different orientation  don't
> contain any read sequences. Contigs built from the reads of the same
> orientations are fine.
>
> Your help/advice would be greatly appreciated.
>
> Cheers,
>
> -- 
> Jiri Stiller
> Senior Bioinformatics Researcher
> Australian Centre for Plant Functional Genomics
> School of Land, Crop and Food Sciences
> University of Queensland
> Brisbane QLD 4072
>
(Continue reading)

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