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Old 03-07-2011, 07:06 PM   #1
chronix
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Default how to remove N (gap) in sequences?

I need help. How to remove N between in sequences using by velvet?
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Old 03-07-2011, 07:25 PM   #2
Rachel
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Hi i am about to ask the same questions. I had some the NNNN between my sequences and I had done some PCR to close the gaps. In this case do anyone know what type of software to remove the NNNN and replce it with new sequences?

Thanks
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Old 03-08-2011, 05:07 AM   #3
Peter Bjarke Olsen
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You can avoid the N's in the velvet output by using the -scaffold option when running velvetg.

Best regards,

Peter

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I need help. How to remove N between in sequences using by velvet?
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Old 03-08-2011, 05:31 AM   #4
Peter Bjarke Olsen
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One solution could be to use the obtained sequence together with velvet using the -long option.

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Originally Posted by Rachel View Post
Hi i am about to ask the same questions. I had some the NNNN between my sequences and I had done some PCR to close the gaps. In this case do anyone know what type of software to remove the NNNN and replce it with new sequences?

Thanks
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