[maker-devel] 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 <maker-devel-bounces at yandell-lab.org> on behalf of Xabier Vázquez-Campos <xvazquezc at gmail.com>
Date: Monday, October 23, 2017 at 5:03 PM
To: Emmanuel Nnadi <eennadi at gmail.com>
Cc: Maker Mailing List <maker-devel at yandell-lab.org>, "Ence, daniel" <d.ence at ufl.edu>
Subject: Re: [maker-devel] Contamination report from NCBI

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 <eennadi at gmail.com<mailto:eennadi at gmail.com>> 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.
Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications

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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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