Errors in RosBREED alignments

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Errors in RosBREED alignments

Hussié
Hello,

I noticed an error concerning the RosBREED reads details. The FASTA
sequence appearing in the bottom of the page should be the read's one
according to the sequence identifier. However, what is displayed is
actually the scaffold sequence that matches with the read. This error
can be unnoticable for reads that match perfectly with the reference
sequence but it is clearly visible for reads like this one :
> http://www.rosaceae.org/gb/gbrowse_details/prunus_persica?ref=scaffold_2;start=4858736;end=4858808;name=HWI-EAS121%3A5%3A37%3A1256%3A1338%230;class=match;feature_id=HWI-EAS121%3A5%3A37%3A1256%3A1338%230%3B1%3B4858736%3B4858808%3B1;db_id=okinawa%3Adatabase
I hope this suggestion will help improving this already really helpful tool.
Sincerly,

Hugo HUSSIE

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Hugo HUSSIE
INRA GAFL, Domaine St Maurice, CS 60094, 84143 MONTFAVET
Tel: 04 32 72 26 67
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Re: Errors in RosBREED alignments

Scott Cain
Hi Hugo,

Thanks for pointing this out.  The sequence at the bottom of the gbrowse_details page is never for the read, always for the scaffold or chromosome, but I agree, using the id of the read in the fasta line is wrong.  I'm going to submit this as a bug so it doesn't get lost:


Scott



On Tue, Sep 17, 2013 at 4:44 AM, Hussié <[hidden email]> wrote:
Hello,

I noticed an error concerning the RosBREED reads details. The FASTA
sequence appearing in the bottom of the page should be the read's one
according to the sequence identifier. However, what is displayed is
actually the scaffold sequence that matches with the read. This error
can be unnoticable for reads that match perfectly with the reference
sequence but it is clearly visible for reads like this one :
> http://www.rosaceae.org/gb/gbrowse_details/prunus_persica?ref=scaffold_2;start=4858736;end=4858808;name=HWI-EAS121%3A5%3A37%3A1256%3A1338%230;class=match;feature_id=HWI-EAS121%3A5%3A37%3A1256%3A1338%230%3B1%3B4858736%3B4858808%3B1;db_id=okinawa%3Adatabase
I hope this suggestion will help improving this already really helpful tool.
Sincerly,

Hugo HUSSIE

--
Hugo HUSSIE
INRA GAFL, Domaine St Maurice, CS 60094, 84143 MONTFAVET
Tel: 04 32 72 26 67
[hidden email]



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2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13.
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Ontario Institute for Cancer Research

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