Contamination report from NCBI

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Contamination report from NCBI

Emmanuel Nnadi
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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Re: Contamination report from NCBI

Xabier Vázquez Campos
Hi there,
Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.
I would seriously encourage you to redo the assembly before continuing.

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,
Xabi


On 24 October 2017 at 00:30, Emmanuel Nnadi <[hidden email]> wrote:
Hello

Good day.

Please I submitted my sequence to NCBI and they sent back this contamination report.

Please how do I use maker to effect the correction


Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.

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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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Re: Contamination report from NCBI

Fields, Christopher J

It looks like the adapter is primarily at the ends, which is easy to remove.  However, I agree, removing these and redoing the assembly may improve the assembly quality.

 

chris

 

From: maker-devel <[hidden email]> on behalf of Xabier Vázquez-Campos <[hidden email]>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <[hidden email]>
Cc: Maker Mailing List <[hidden email]>, "Ence, daniel" <[hidden email]>
Subject: Re: [maker-devel] Contamination report from NCBI

 

Did you perform quality and adapter trimming of your raw reads? That's actually an assembly issue.

I would seriously encourage you to redo the assembly before continuing.

 

If that isnt possible, start by removing those sequences and split the contigs at those places as suggested in the report.

For the annotation part, not 100% sure but I'd say start with the "Merge/resolve legacy annotations" steps but maybe Carson or Daniel have a different suggestion
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Merge.2FResolve_Legacy_Annotations

Cheers,

Xabi

 

 

On 24 October 2017 at 00:30, Emmanuel Nnadi <[hidden email]> wrote:

Hello

 

Good day.

 

Please I submitted my sequence to NCBI and they sent back this contamination report.

 

Please how do I use maker to effect the correction

 

 

Nnadi Nnaemeka Emmanuel

Department of Microbiology,

Faculty of Natural and Applied Science,

Plateau State University, Bokkos, Plateau State, Nigeria.


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maker-devel mailing list
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--

Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA


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Re: Contamination report from NCBI

Martin MOKREJŠ
In reply to this post by Emmanuel Nnadi
Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this contamination report.
>
> Please how do I use maker to effect the correction

--
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/

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Re: Contamination report from NCBI

Emmanuel Nnadi
Thanks! 
Nnadi Nnaemeka Emmanuel
Department of Microbiology,
Faculty of Natural and Applied Science,
Plateau State University, Bokkos, Plateau State, Nigeria.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

   

On Oct 24, 2017 11:23 AM, "Martin MOKREJŠ" <[hidden email]> wrote:
Hi Emmanuel,
  use trimmomatic or cutadapt to remove the adapters and check the output file for unremoved cases. Once they are all removed redo the assembly.
Martin

Emmanuel Nnadi wrote:
> Hello
>
> Good day.
>
> Please I submitted my sequence to NCBI and they sent back this contamination report.
>
> Please how do I use maker to effect the correction

--
Martin Mokrejs, Ph.D.
Adapter/artefact removal from datasets based on the following technologies:
  454 / IonTorrent / Evrogen MINT / Clontech SMART / ..., Illumina
http://www.bioinformatics.cz/software/supported-protocols/

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maker-devel mailing list
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