Map with Bowtie for Illumina (version 1.1.2)

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Map with Bowtie for Illumina (version 1.1.2)

KNIGHT M.R.

Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in –v alignment mode/ If so, what settings do I need to enter? Many thanks, Marc.

 

 

***
Professor Marc R. Knight,
Director,

Durham Centre for Crop Improvement Technology,

School of Biological and Biomedical Sciences,
Durham University,
South Road,
Durham DH1 3LE.
Tel: +44 191 33 41224
Fax: +44 191 33 41201
Website: http://www.dur.ac.uk/dccit/
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Re: Map with Bowtie for Illumina (version 1.1.2)

Dannon Baker
Hi Marc,

Yes, if you change "Bowtie settings to use" from common to full, you'll see the entire parameter list, including "Number of mismatches for SOAP-like alignment policy (-v):"

-Dannon

On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote:

> Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in –v alignment mode/ If so, what settings do I need to enter? Many thanks, Marc.
>  
>  
> ***
> Professor Marc R. Knight,
> Director,
> Durham Centre for Crop Improvement Technology,
> School of Biological and Biomedical Sciences,
> Durham University,
> South Road,
> Durham DH1 3LE.
> Tel: +44 191 33 41224
> Fax: +44 191 33 41201
> Website: http://www.dur.ac.uk/dccit/
> ***
>  
>  
>  
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Map with Bowtie for Illumina (version 1.1.2)

KNIGHT M.R.
In reply to this post by KNIGHT M.R.

Hi, I’m trying to assemble Illumina paired sequence which is at least 15x deep to the Arabidopsis genome (TAIR 10 version) using Map with Bowtie for Illumina (version 1.1.2) but try as I might with changing all the parameters in different ways to reduce stringency I am still getting a lot of gaps in the assembly (probably about 10% missing).  What settings would you advise I focus on to try and improve the situation?  Many thanks in advance! Marc.

 

 

***
Professor Marc R. Knight,
Director,

Durham Centre for Crop Improvement Technology,

School of Biological and Biomedical Sciences,
Durham University,
South Road,
Durham DH1 3LE.
Tel: +44 191 33 41224
Fax: +44 191 33 41201
Website: http://www.dur.ac.uk/dccit/
***